Not sure what you mean by throwout shaft. Measure the length of the bearing retainer coller on the old trans. & cut the T-5 to match. It cuts easily with a hacksaw after removal. Cut the end of the pilot shaft to match the old one with a cutoff wheel.
Slide the clutch disc on the input shaft till it stops. Mark it. Grind the grooves till it will slde on about 3/8 to 1/2 farther.
Drill the mounting holes out to 1/2 in. That should get it.
Dont get discouraged. There is a lot of info out here on this & the results a gratifying.