I went through the same thing a year or so ago. I did the initial clutch swap myself and afterward shifting went to )%*)$!
Having done a lot of clutch replacements in the past and even after going back through everything finally had to throw hands up in the air. Out of time to do on my own I took it to Sports Car World in Dallas. The brand new clutch had a manufacturing defect. Sent back to JAE and they swapped it out. I also had SCW adjust everything from front to back. My 1994 S4 shifts as good as any car I have ever had, like butter, now.
Kenny; Dallas Tx
1995 Lexus SC300 - SOLD
1990 Nissan 300ZX - SOLD
1990 Nissan 300ZX Twin Turbo - SOLD
1996 Porsche 911 Cab - SOLD
1989 Porsche 928 S4 - SOLD
1994 Lotus Esprit S4
Test pipe, Ramspott & Brandt center exit exhaust, 2002 center exhaust valance, Alunox performance exhaust manifold, Spax coilovers with Eibach front springs, Elise steering wheel