Roland, Here is what you need to do. You will need to grind down the mounting boss on the trans side, even with the mounting bracket. This is only true with the 3spd, the 4spd has no boss to worry about. The pedal bracket should now bolt up to the bell housing just like before. I didn't worry about the original mounting point that went into the side of the 3spd. Just make sure you use grade 8 bolts for the three mounting points into the bell housing this will be enough to hold the pedal assembly and the master cylinder. Check out John Sandoval's tech tip on the T5. Lots of good info there.
Now for the master cylinder. I used a dual master from a 69 mustang, which works real well. I had to fab a bracket to mount it but it isn't hard to do. I've got some pictures and a small write-up I can email you if you want it. Just shoot me an email and I'll get it to you.
George
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