Don't separate the OD and trans if you don't need to. I expect you did this, but the drive plate needs to be aligned with a centralising tool before the cover plate is tightened down. If the drive plate is even a small bit out of line the gearbox shaft won't present to the pilot bearing correctly. Put the gearbox in top gear, you can then twist the output by hand to line up the shaft splines with the drive plate splines.
Flange bolts always a pain as a standard open ended spanner won't fit properly. Small thin, straight ring spanners work well. Nuts and bolts often rounded off so having new ones for the refit makes the job easier and less frustrating. These bolts are special for this application so buy the right ones.