What's causing this gear grinding

[UndergroundR32]

I'm going to give a basic run down of what happened. About 1600 miles ago the car was built. My mods are in my profile, but the only relavant mods for this question are that I bought a used stock flywheel and had it resurfaced like you should always do with a used oem flywheel. I mated that to an ACT 2600 clutch which were both resting on a used crankshaft that I had knife edged, NOT cut. The machinest is a local guy who builds race motors quite often. Though they are mainly V8's he has done 4g63's for a number of different customers. Also I had a nearly new (less than 500 miles) 1992 Galant VR4 transmission that I sent to John Shepherd for a race rebuild with some other extras.
My issue is that shortly after the 500 mile break-in of the Clutch/Engine I began grinding 1st, 2nd, and 3rd gears from time to time. 3rd gear grinded almost everytime I shifted quickly at any RPM, but 1st and 2nd would grind despite shifting speed or engine RPM. So I pulled the transmission just recently and had it opened up with the intentions that I may possibly need to replace my 3rd gear synchro. But to my suprise, the gear sets and synchros were almost mint. My clutch was adjusted and my slave cylinder and clutch master were both functioning properly. My question is both what do you think is causing this, and is it possible that the used oem flywheel may have been cut too many times and is causing problems?

 

[paranoidTSi]

I was grinding in 1st and 2nd quite often, and I couldn't get into 1st without being below 5MPH. I replaced the clutch, NO gear grinds but 3rd..which seems to be a common DSM problem. You could try Sychromesh if you'd like, reportedly it works pretty good.

 

[UndergroundR32]

No, this is definately a problem somewhere else. I can't race because of how often 3rd gear grinds. If I shift at 7800 rpm or so it'll grind terribly and possibly not even go in.