You know I have had similar problems on my 2nd gen. I think there's two things going on in my case:

1)The new synchros seem to take forever to bed in. 1000+ miles. I don't know if this was a material change. They may have upped the hardness on them to prevent wear, but this makes theme take longer to bed. The new three piece synchros had a 2004 date stamped on them, so this couldn't have been a recent change.

2)From the trans shifting like crap I have gotten really ginger shifting it. I think as you seem to be speculating if you try to shift quickly without enough force the synchros keys don't apply enough pressure and you get a scratch or notchyness. I have noticed if I shift REALLY slow and gently sometimes into 2nd at like 10 mph you can feel it go past the dogteeth a couple teeth before completing the shift. I think I just need to train myself to shift harder, but its difficult when your trans hasn't worked right for 3 years.