I have a Tremec TKO with a Lakewood SFI bellhousing w/ block plate.
I had to shorten the pilot on the input shaft to get things to mate up properly.
I had measured and adjusted everything else and could not get the engine and bellhousing to mate up.
After a bit of head scratching, I checked the pilot hole depth in the crank and found the problem.
It's easy to overlook something like that.
I used a cutoff wheel to shorten the shaft and carefully deburred and chamferred it and all fit up nicely.
Be careful and use plenty of water when cutting the shaft. You don't want to get it too hot or you'll affect the temper.
Also be sure to check your clutch lever adjustment. Make sure the geometry is correct and that you'll have sufficient travel to fully engage and disengage the clutch.
Measure everything twice, cut once.
Hope this helps,
David