When you replace the cover it needs to be fairly hot so it slips over the bearing races with out pounding. I was doing the epoxy measuring method and forgot this piece of advice. I got the cover on by banging with a rubber mallet. I baked it in an oven per directions and removed the cover. There was Zero clearance for the input shaft shown by the lack of epoxy at the input bearing. I thought this odd but put my trans together this way and later realized the error of my thoughts. By banging the cover on the input is able to bounce up and down. It is not held the same way as the other shafts, I got measurements on the other two shafts. I got Zero on the input. I used that trans for 6 months but it never worked right. So I still have it and plan to fix this someday but I am using another trans right now.
The epoxy that I was given to do this was not a two part item. It was set by heat. I didn't like this anyway. The finished epoxy was not as hard as steel, it was difficult to measure because it could bend a little.
I've heard that solder works better but never tried it.