1981 KZ550 Exhaust headers 3&4 are running colder than 1&2

The PO had installed a Dyna S system prior to me getting the bike. You think they could've installed it incorrectly and that may be causing the issue?

Yes. If they messed up the plug wiring, they could easily have messed up the advancer.  It's easy to check so might as well check.  It's a relatively easy fix to correct it.

With a Dyna S, the rotor has a magnet that looks like a little round spot on the side of the rotor.  That round spot should point toward the side with the aforementioned "TEC" logo.