Got a lot of free play at the top of the throw of the pedal? My master cylinder was sitting ok in the socket of my 99.5 with the exact same symptom you describe. But it was shifting in and out about 1/16 inch. Now don't laugh but this worked for me. I found some baling wire and carefully wrapped the cylinder right underneath the little ears that stick out to shim the cylinder a little higher in it's socket. That move alone brought the pedal engagment up about halfway up off the floor. MUCH improved shifting, lot's easier to get into low gear while stopped, etc.