John,
Dumb questions: are you sure you got the correct throwout bearing?
I had to replace the front bearing retainer in mine which required machining a retainer for a Ford application. Luckily, I had the correct bearing to use for measurements.
Our 3 speeds use an input shaft diameter that's in between the small and big block Ford diameters, which makes things fun.
You may have the correct trans with a different retainer.
Good luck.
-Joe