What do you have for tranny mounts ?
You may have too much movement in the driveline, which is not helping the shifter and linkage stay aligned.
I'm just a big fan of limiting the amount of slop on the drivetrain.
I know when I put the STI rear tranny mount in my wagon it made a world of differance under high rpm shifts. Not so much of a differance when I put the same mount in my 09 Spec B.
174,000+ miles, 5/20/12 new ej257 short block, 8/20/11 installed VF52 turbo, @20.8psi, 280whp, 300ftlbs. Also CHECK YOUR OIL, these cars use it.