Ok, so how LONG is a long time for it to sit? And why was it originally in pieces? You can pretty much guarantee that the carbs have some sort of schmeg gumming them up. Especially if we're talking YEARS of sitting.
When you dropped it in first gear did it stall immediately like the ignition was cut? Or did it slowly die while trying to let the clutch out? Also, you said you got it running again, did you ride it or did you just get it to idle again? It's possible that the clutch plates were stuck together, thus stalling the engine. On the other hand it could have been the clutch or side stand switch (which would be similar to the clutch being stuck).
I imagine with the overbore and hot cams/valves that something was done to the carbs. Unless there were some FCR flatslides removed prior to you picking it up. Most guys ditch the stock carbs in favor of the FCR flat slides when building a motor as you describe. And I say most because I kept my stock carbs when I built my 1024cc 93 RR to maintain street driveability.
What other type of parts needed replacing? You mentioned harness and rear brakes, but that's a pretty broad spectrum. If you don't have one already get a manual get one. They are a rebuilders bible IMHO.
If possible get a compression check done. That will give you some idea if the rings and valves are seating good enough for combustion. Could be more than just a carb issue. But when you do clean them, make sure you take every screw out that can come out. All too often carbs aren't broken down enough to clean every minute orifice properly.
Toss up some pics of your bike, too. We love bike pics here. Oh, and