If the pins and sockets create problems, I first try to fix them. Usually, drilling the socket hole a bit bigger and deeper fixes the two main problems, slight registration errors, or pin bottoming out in socket. If that still does not fix problem, or if kit lacks pins, I use slow drying glue and do best I can.
One big problem that has no easy fix is when the height of one side of the kit is different than the other side. In that case no amount of shifting can eliminate the steps, only minimize them. Sometimes a couple of those new clamps with micro adjustments can reduce the problem by creating just the right amount of squeeze on the larger side, but never seems to eliminate the steps entirely. Lots of scraping, filing, and filling are the only recourse on these kits.