I'm at Romraider tuned Stg 2... TBE, TMIC, Prodrive CAI. I'm saving up for a 6 spd swap or PPG's. Haven't decided yet. 25,000 miles, been stg. 2 since 2,000 miles. No problems to report, except a intermittently squeaking throwout bearing since 7,500 miles.
I had a 2004 WRX, Cobb stg 2 for ~20,000 miles, no transmission problems at all...
Friend has a 2004 WRX, stg 2 for ~50,000+ miles, no transmission problems. (although there is a nasty squeal noise now and we think it's an exhaust gasket)