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Ok gentleman. I am going to try to get the pictures posted on how to rebuild a 2000 RC 51 Honda motor downloaded for you to view.
Some background is I have been a mechanic for 20+ years and owned a motorcycle shop for a few years. Have been building custom bikes for the past few years and thought any information I would post maybe save you some money in the long run.
This is a guide only. As always, refer to the service manual for your specific motorcycle.

Picture 1 is the lower engine case half placed upside down. I blasted all cases with walnut shells and thourghly cleaned with solvents and compressed air. Masked off flanges and clearcoated cases and cylinders to prevent oxidation and should help with washing the motor later on. Honda used to clearcoat their motors in the 70's.
Picture 2 is chasing (cleaning) the bolt holes with a bottom tap. Make sure not to break the cases by going farther then the origional thread depth.

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The oil pump is very important. Please don't just put the pump back in place without visually inspecting all rotating components and checking the clearance between the inner and outer rotors. Oil all moving parts before installing in lower case.

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It is a good idea to clean all mating surfaces with a Flat stone and clean with a degreaser. I used lacquer thinner to clean the mating surfaces

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I had the cylinder bored to o.e.m. specs at .025 over stock. This pic is to show you it is very important to clean the cylinders with a clean oiled rag. This will wipe out all boring grind dust and fragments untill the rag comes out clean. A CLEAN cylinder is a happy cylinder .

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Picture 1. Important to check all oil passages to make sure there is no obstruction. I used compressed air to blow thru all oil passages and visually inspected.
Picture 2. Probably a good idea to place new piston side by side of old piston. Remove from rod and install new piston on rod. Note: Important to make sure you locate (IN) and (R) and (IN) and (F). R stands for rear piston and F stands for front piston.
By placing the pistons side by side you would of already matched the rod oiling holes properly prior to installation of pistons in upper case half.

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Pic 1. Prepare Crankshaft for installation. Check bearing surfaces for any abnormal wear. Replace Starter driven gear bearing on crankshaft. Apply some heat with a propane torch. The bearing race will come right off. Heat the new bearing race lightly. Do not over heat it will turn blue and damage it.

Pic 2. Install the pistons. They are marked Front intake and Rear intake. It is best to use a ring compressor as to not damage the rings.

Pic 3. Install the tranmission per instructions in the service manual. My transmission shifted great prior to disassembly. So I left is together on the work bench. I did visually inspect all gears and cogs. Notice the white line areas on the picture. These areas should be coated with Yama Bond Sealant. Do NOT get any Yamabond on the areas marked in RED.

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NOTICE: MOST PICTURES HAVE DETAILS ON THEM. CLICK ON THE PICTURES FOR MORE VISUAL DETAILS.

I Replaced all my rod and crank bearings just because I wanted a strong lower end of the motor.

pic 1. Install lower crank bearings and install crank. Make sure you install the crank so the fly wheel side is facing left on the crankcase. Do not oil the bearings just yet. We are going to check the clearance with plastic gauge.
Intall a thin strip of plastic gauge on rod. Install bearing caps.
Pic 2. Torque to 22 ft lbs +120 degrees.

Pic 3. Remove bearing caps and check plastic gauge for proper clearance. Service limit is .0019 in.
As always apply oil to all bearing surfaces. Install bearing caps oil the threads on the bolts and torque to 22 ft alb a+ 120 degrees.

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pic 1. Install oil orifices in upper cases. It will be easier to align this way when the cases are put together.
Pic 2. Measure the connecting rod side clearance with feeler gauge. Service limit is .016 in.

Put both cases together make sure yama bond did not get on any bearing surfaces. Should be easy to clean because we put it on about a half hour ago. If surface is to dry reapply yamabond. No picture putting cases together. I needed both hands. Carefully put cases together might have to wiggle cases and put a light amount of pressure on them to go together all the way. This is not easy aligning all the dowell pins and oil orifices. Took me two trys. The cases will go together. With out using a hammer.

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Pic 1. I decided to show you again where the dowell pins are located. I actually took them out of the lower cases and installed then in the upper cases. Manual says to lower upper case onto the lower cases. However I thought it would be easier to align the oiling orifices in a round hole rather then in a semi round with a flat surface. Therefore I put all dowells in the upper case and lowered the loweer case onto the upper case. I hope I didnt confuse you.

Pic 2 Install all case bolts. Take note of what color bolts and length when dissassembling. Will help when you reinstall them. Snug bolts donot tighten yet.

Pic 3. Install mainshaft seal plate. Apply locktight to threads. torque to specs
Now torque all case half bolts in a crisscross pattern. Black bolts 38 ft lbs, grey bolts 14ft lbs +120 degrees. 10 mm bolts 29 ft lbs.

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here is picture of dowell pin locations. Important not to forget any.

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Pic 1. I installed new shift shaft, clutch rod, and sprocket seals before cases were put together.
Only one case bolt requires a sealing washer.

Pic 2. Apply thread sealant on the oil pressure switch and install. Will help stop any debrea from falling into main crank shaft bearing.

Pic 3. New sealing washer on gear selector switch and install shift shaft seal holder.

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We are still on the left side of the engine.

Pic 1. Put Oil on starter driven gear and sprag clutch and install.

Pic 2. Put oil on starter idler shaft and gear and install. Also install torque limiter. Next I rotated crank to have the keyway slot for the rotor in the 12 o clock position. Place half moon key in slot and place flywheel in place. I used a strap wrench to hold rotor while torqing to 116 Ft Lbs.

Pic 3. Install new o-ring on starter motor and installed. You may have to rotate flywheel a little to align the starter teeth to go in place. Torque the 2 starter bolts

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Right side of engine

Pic 1. Install washer on shift shaft and oil shaft. Slide in the case check to make sure it is aligned with the seal on the other side of engine.

Pic 2. Install clutch basket with oil pump chain and sprocket. Note: Slots in pump shaft align with sprocket. Apply lock tight to bolt and torque.

Pic 3 Inspect dampner springs in primary drive gear. Make sure washer is in place and align the holes. when putting back together.]

Pic 4. Rotate crank so wide tooth on shaft is at 12 o clock. Install timing gear.

Pic5. Install primary drive gear assembly. Install special washer and LEFT hand threaded Bolt. Torque to 65 Ft Lbs I used strap wrench to hold flywheel.

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Installation of Timing gears

Pic 1. Clean both cylinder gasket surfaces. Install the water jacket sealing washers. This is impossible once the heads are bolted in place. so do it now.
Pic 2. Install both cylinder head base gaskets and dowell pins. the gaskets come marked F for front and R for Rear cylinder.
Pic 3. Install both cylinder timing gears and the 4 bolts per gear. Snug only you will torque later in next step.
Pic 4. Install the last 2 timing gear bolts with a sealing washer. Now you can torque all bolts. should be 10 of them total. Look at pics for torque values.

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Installing Cylinder heads
Manaual specificaly tells you to install the front head first.

Pic 1. Rotate flywheel counter clockwise to align the timing mark to F T. The front piston will be at the top of cylinder. Also refered to as TDC top dead center.
Pic 2. Front Cylinder is ready for head. Timing gears secured, head gasket in place.
Pic 3. Make sure the two dowell pins are in place. Lower front head onto cylinder base. Apply oil to the threads and seating surfaces of the 4 @ 11 mm cylinder head bolts and install them. Torque to 51 ft lbs in a crisscross pattern. On the outside of head Securely tighten the 2 @ 6mm bolts

Before you install the valve shims measure with a sliding caliper or 0 to 1 in micrometer the thickness of the shims. Write these measurements down on paper. You will need these dimensions later on when adjusting the valve clearance.Lightly oil valve springs. Install shims in thier origional place.

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Install front cams
Pic 1. Apply oil and install valve lifter caps in their origional lifter bores. Make sure they slide up and down freely. It has been know that some machinist will damage these bores when servicing heads.
Pic 2. Locate the Front cams they are stamped from the factory. FR IN = Front cylinder intake. FR EX = Front cylinder exhaust.
Pic 3. Now double check to make sure flywheel timing marks are at FT. You can also look down spark plug hole to verify piston is at T.D.C. Top Dead Center.
Lube cam journals and cam. Install cams, The alignment marks on the cams should be facing outwards and aligned with top edge of head.

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Install front cams continued.

Pic 1. Install cam holders. They are marked simular to the cams FI Front intake and FE Front exhaust. Torque to 17 Ft lbs in a crisscross pattern.

Pic 2. Check valve clearance with feeler gauge. Intake .006 +-.001 Exhaust setting should be .012 +-.001. Record your readings. Now rotate flywheel several revolutions, then set timimg marks back to FT and recheck timing gear marks and valve clearance. You should have the same readings as before that is if everything is put together correctly.

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Adjusting the valve clearance.

Pic 1. The shims come in 51 different sizes from 1.200mm to 2.450 mm in intervals of .025.
Here is a formula to help calculate any adjustments needed to stay within the recommended tolorances.
Remember intake valve clearance .006 +-.001
Exhaust valve clearance .012 +-.001

A = (B - C) + D
A: New shim thickness
B: Recorded valve clearance
C: Specific valve clearance
D: Old Shim thickness

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Install Rear cams and check valve clearance. Please follow this procedure closely.

Pic 1. Start out aligning the flywheel timing marks to FT.

Pic 2. Front cam marks facing outward with index lines parrell with head.

Pic 3. Now rotate the flywheel counterclockwise 3/4 turn or 270 degrees to align the RT marks Verify the rear piston is at Top Dead Center.

Next, Install cams using the same procedure as I did the front cylinder. Review the last 4 post and start with installation of timing gears. All measurements will be from the fly wheel set at RT. install cams and check valve clearance.

Pic 4. Always a good idea to cover motor when not working on it.

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Install oil pan.

Pic 1. Install oil pan pick up tube with rubber washer. Install the return line tube with o ring and oil pan.

Pic 2. Slot in oil pick up tube needs to be aligned with slot to be able to go in all the way.
Right side of engine,Install clutch basket
Notice holes on back side of clutch basket, they align with the pins on the oil pump drive sprocket.

Pic 3. Outer clutch basket installed to include special washer.

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Installing the Clutch

Pic 1. Intstall clutch inner hub. Concave washer and nut. Torque to 94 ft lbs. Stake the nut in the recessed area of shaft.

Pic 2. Soak clutch plates and fibers in oil. Notice the first and last fiber is blue. They are different part numbers than the red ones.

Pic 3. Install clutch, springs, and bolts. Torque to 9ft lbs.

Pic 4. Install clutch case and water pump housing. If you replace the water pump seal make sure impeller doesn't rub the outer housing.

Pic 5. Fill all fluids.

I will be posting a link to You Tube with the motor running when I finish the wiring.