gear box

I'm working on a ZD28 with an RCKP - 72" deck. I am replacing lower bearing(output) and seal in the gearbox, and replacing the holder underneath. My question concerns the shim placement inside the gearbox. I didn't pay close attention on how many shims were in one hole as opposed to another. I have one hole for sure holding 2 shims. If I read the parts list correctly, it shows 2 shims on the output shaft. I'm positive there was only one shim in there when disassembled...and the shim looked a little worn on one side. The output shaft was loose, it would move around a little making me assume it was a bad bearing. The bearing was still good, the seal wasn't, and everything below that was gone....no grease.
My concern is how to tell where a shim is needed. The output shaft is still a little loose, not sloppy loose, but it doesn't seem right.....Any ideas?