I ran into a problem when rebuilding all the System 6 boards for my Blackout where the connectors were trimmed too close to the board. It made it almost impossible to properly re-solder. The 40-pin connectors between the boards were all replaced with new connectors. For the rest I used this tool I designed to fix the connectors. I remove them all, put this spacer underneath, then lightly press them in the vise to push just a tiny bit (1/32") through the shell. It lines up all the pins nicely and only takes a few seconds for each connector. I use a vice with flat jaws and a business card taped to each side. That keeps the pins from flexing when tightening.
Once done I go over the solder side of the pins with a wire brush on the dremel and they are ready to install. There is just enough exposed to make a nice solder filet for a strong joint. Doesn't affect where the connectors plug onto the board at all.