Hey Matt,
I would check the thickness of the crank web were you will have to press in your relocated pin, you will find on 1 web the thickness is half of the other!
Also the transmission is built tougher than the nsr250 box but I doubt it would handle 120+ hp for long. Honda shorthened the engine by having all three selector forks on the one shaft making it shorter than an rgv250 engine for example, however this may also allow a little more slop and lack of precision under extreme (as 3 yz250's would be!) power shifts. They also didnt machine the grooves in the selector drum far enough resulting in slipping gears because the forks are not pushing the gears in far enough thus bending shifter forks and eventually jumping gears. With shimming I believe this can be resolved and I am putting a modified transmission on the road this xmas for testing.
The clutch seams to slip when on slightly modified bikes although from all reports the ebc heavy duty clutch fixs it. According to part numbers its the same as a 900 fireblade so It may just be the springs.
Good luck with whatever you decide, gotta love that v3.
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If all else fails - gas it!