Given that this problem appeared immediately after the installation of the Pmags (please correct me if not accurate), it would be difficult to assume the problem is unrelated to the installation. I imagine it is possible that the owner disturbed the intake gaskets or something else during the installation. However, given the immediate onset of the problem, it seems logical to focus on what has changed. I'm sure he could improve the baffles, but what are the odds they just started leaking the day he installed the pmags. Same with fuel flow. If the temps were normal before the installation, I can't imagine drilling a jet is going to fix the new problem on #3.
I would spend some time thinking about everything that I touched when I did the install. Have you had the cowl off since? Maybe a baffle seal was kinked or out of position, maybe a rag was left on top of the cylinder, etc. Has someone confirmed that the timing was set properly. It wouldn't be the first time that someone timed the ignition incorrectly on a Lycoming. Did you confirm that each sparkplug was tightened, etc. Also, I don't believe you are looking for a lean condition on #3. Lean cylinders don't show these types of disparities. If the other three cylinders are under 400 and let's say 100* ROP, you won't see a 50 degree increase in CHT by leaning to peak from 100 ROP (Peak CHTs occur at approx 80 ROP and will fall on either side of it). I don't know what the typical CHT spread is between 250 ROP and 80 ROP, but I can't imagine it is 50*. Maybe someone else can chime it, I don't ever run that rich. Detonation is a more likely culplrit for this type of spread. Detonation is most often caused by timing issues, going back to what has just changed.
Good luck,
Larry