I measured my own before I removed the bearing.... From the absolute end of the jackshaft to the closest inner race was exactly 95.3 mm.....or 3.752 inches.....
I'm almost certain that these measurements are the same for many different models and years since the part numbers are the same....
My sled was a 500 VMax 1999, but the Yamaha manual sold to me by Yamaha is for sleds from 97 through 99.....
Can you see where the set screws pinched the shaft?...
Also.... What if you were to assemble everything together from the chaincase side to the PTO side first..... Then when all finished, tighten the set screws for the bearing on the PTO side last.... This would ensure proper placement of the bearing....
If the distance isn't 95.3mm or 3.752 inches, then please let us know...
TJ