Rebuilt 904 w/ tf2 shifting woes...

I'm no auto trans expert, but the factory settings and recommended adjustments are all to get close to certain settings. Might not hurt to verify your pressures to ensure something internal didn't go haywire, especially since your valve body is modified. Possible a minor issue is causing a pressure loss at the wrong time? Again, I'm no expert on autos... But seems like something worth ruling out.