Shaft bearings question and transmission flush?

Just bought the boat but it had a rubbing sound at low rpms in forward. So we decided to pull the shaft and replace the bearings. So you know it's a 1987 mastercraft tristar 220. As we got in there I found that there are no bearings, just a couple of rubber couplers, the shaft has had a pretty bad leak for quite a while, and I'm wondering if there has been some sort of upgrade, or if I just want to replace some parts, Thanks.

-P.S. While we have been cleaning thing up, we pulled the transmission out, and some other parts, they had been used in saltwater and were incredibly corroded, we got them sand blasted and are repainting them, they look brand new now. Here's question #2, What is the best way to flush out the transmission? It is currently out of the boat so what ever you think works best. Thanks.