a 1963 toploader 3-speed bearing retainer and the hole in a mid-70's 4 speed bellhousing? The hole in the bellhousing is 1/8" larger than the bearing retainer. I will re-drill and tap the holes for the small pattern trans, once the trans is properly located in the bellhousing.

Your best bet would be to have a machine shop make one for you.
It would have to be pinned into the housing so it wouldn't move out on you.

Does your three speed have a synchro first gear?
If not, then switch to the fully synchronized three speed.
Don't do it for the synchro - do it for the strength - that non-synchro three speed is much too light duty for your application.

It's from a 1963 390 Galaxie. How much tolerance should be between the bellhousing, spacer, and bearing retainer?

The spacer should be press fit into the bell housing but .003" +.001" -0" for the retainer. It centers the transmission and crankshaft so it is a critical tolerance.