If it were me I would check that all the fuses are correct then look over the wiring to see if something looks odd or wrong and plug it all in and test it out. If nothing looks hacked worst case is things just won't work. Then see whats working and whats not and go from there.

Worst case scenario is a coil or display 'locks on', but as long as you're looking out for it, and turn off the machine on the off chance it happens, you're not going to damage anything. Most machines work fine without any repinning, it's just a best practice

For the most part, pins are replaced because they are too tarnished or don't have enough tension to make proper electrical contact with the contacts on the edge connectors on the boards.

If you're missing a ground connection, then it could potentially cause problems that cause damage, but I haven't experienced it first-hand. You can do a continuity test to check for this.

After that, the worst that can happen are missing signal or voltage lines that cause the game to malfunction in minor or major ways (but which also can be corrected).

I usually do, but you may be able to get away with not doing them since those connectors are rarely disconnected and don't suffer from some of the same problems you see on the other backbox connectors that are usually disconnected whenever the game is moved.

Also--you can (and should) re-use the plastic edge connector housings. They are starting to get scarce, and there's usually no point in replacing them since there's usually nothing wrong with them.