Were you using the xr shaft or the ex shaft? If I remember correctly the ex shaft was not quite as long and didn't extend fully through the idler gear and into the case. I seem to recall having the same issue and switched to the xr shaft and didn't have any more problems. Also when I talked to steve#7 he was running very high compression without any issues. Just some food for thought
2000 440EX Powroll Stroker, 39mm FCR, Ported & Polished, Hot Cams Stage 3, Full Curtis Spaks X-6 Exhaust, 8 plate Sparks clutch, Pingry Oil Tank, K&N Filter, Aluminum Air Box, Renthal Bars, Propegs, Graydon Bumper, Graydon Case Saver, Houser +2's, LSR Axcaliber, Braided Brake Lines, Elka Triple Rates, Mac Daddy Rear Shock, Maier Shiny Race Plastic, Houser +1.25 Swingarm