Most bikes use a shifter drum as the "brain" of the gearbox system. This drum has like serpentine cuts in it that through pegs control the respective shifter forks.
Nice explanation, and the photos help too.
The shift lever turns the shift drum which is cammed (your "serpentine" grooves). The shift forks control the three slider gears and are driven left and right by the turning of the shift drum cam grooves. The slider gears have dogs or slots in the sides of them which engage the dogs or slots in the adjacent fixed gears. Being a "constant mesh" transmission, all the gears are meshed together and spinning all the time - even in neutral.
The wear points in the transmission are the points of the grooves in the drum, width of the shift forks, bending the shift forks, wearing the points off the dogs and slots, and wearing an angle into the dogs and slots.
Other things can wear due to poor lubrication or mechanical failure.
For a variety of reasons on most bikes the setup goes awol in 2nd first and sorry to say there is no quick fix or cheap fix.
Second gear wears the fastest due to the very wide ratio and being the most changed gear. Unless you ride everywhere in first you will shift to second every time the bike is ridden. I almost never get into fifth or sixth gears on my bikes, even the 250's.
What i CAN tell you is that there are those that can run forever on a set of fork/pegs/drum...and there are those that will wear it to smithereens in no time flat.
To really take advantage of a straightcut box means that you have to be engine savy,at least to some degree,and the sorry truth is that most are not.
I'm not sure what you mean by a straight-cut box but I absolutely agree, not taking the time to learn to shift gears smoothly and cleanly is going to cost you money eventually. And playing tunes up and down the transmission is one of the true joys of motorcycle riding for me :-)
If and when you have this apart be aware that the tolerances for the pegs and cutouts in the drum are most likely less than you would think.
Other than badly neglected engines I can't recall seeing any significant wear in the shuft drum grooves. Wear will usually become most obvious by the points of the drum being rounded off, usually due to old and dirty oil. The photo is the shift drum from an '86 GPZ250R engine I'm building at the moment for a project. The entire transmission is like new although the engine itself grenaded a bigend, crank, rod, piston, cylinder block, crankcase and head.
This is said drum for an FZR Yamaha that behaved in exactly the same manner you describe. Notice the amount of wear in the cutout? Most hondos look approx the same.
I would probably regard that as damage rather than normal wear.
Another culprit that might amount to the same fault is a bent shiftfork,which is what this drum controls a set of...via said pegs which are hardtailed into each shifterfork...and then of course the "locks"(dogs) on the gears themselves.
Yes, trying to force gears together can bend the forks and wear them away in the groove of the gear. Both of these will reduce the amount of throw on the gear and cause the dogs and slots to wear rapidly as they bounce off each other. As the contact edges wear, the dogs and slots develop a slope so that the harder you load up the gear the more force is exerted trying to push them apart. Since the only thing holding the slider gear in place is the pin in the groove of the shift drum, the point of the cam gets worn away. The wear in your FZR picture clearly shows that the shift fork was so worn that the pin wasn't even reaching the top of the cam slope before the gear dogs were engaging. The wear you see is the slider gear trying to bounce back from the fixed gear. Undercutting the dogs and slots puts an opposite slope on them so that loading the transmission actually pulls the two gears together tighter.
The shiftforks move like plates that are grossly serrated with "teeth" and these plates hook up to the mating set on each gear as you move respective shiftfork.(aka Dogrings)
Anyways. The wear of the shifterdrum in the pic was enough to make said FZR throw second into "neutral"(which it in reality is not) at WOT.