You may still have a tiny bit of air in the MC and depending on the angle that it is mounted, you may not be able to purge it completely. This is why bench bleeding is so important. Raising the front or back of the rig to level the MC will help with bleeding this air. You could also have a MC issue, fluid bypassing the seals inside.
Now for another question.
How close is your exhaust pipe to the MC or brake lines? I have seen several times where the exhaust has been to close causing brake fluid to boil causing brake issues. Rerouting the lines, shielding lines or moving exhaust cured many problems.
As far as manual versus auto trans, I just don't see the correlation.
