Lots of unmentioned things in this post, but let's take a stab at it anyway.
You say that left side (rear cylinder) muffler had a lot of carbon build up on it BEFORE you had it dyno tuned. From what's been posted on this website regarding the 110 engine in stock configuration (heat buildup etc) and the fact that it has a cut-out that essentially shuts down the rear cylinder under some circumstances, Lots has been said on this subject, but from what I've gleaned, the 110 engine in toto runs exceptionally lean. Given that the rear cylinder has a heat issue, (and I'm guessing) is it possible that the stock OEM EFI set-up has the rear cylinder running a littler richer ? If so, with a multitude of issues on the 110 not burning fuel efficiently (see some of Hoists old posts on his "oil burner" tune-ups in Maine) what you did was allow the natural build up of soot and unburnt fuel that would have gotten clogged in the guts of the stock muffs to find it's way out (not a bad thing) When you had the SERT installed and the bike Dyno tuned your tech would have dialed it in so that it burns what fuel the Throttle Body,cams, valves etc deliver to the cylinders and your issue with soot (carbon) build-up ended. It would seem now all you need to do is buy a can of oven cleaner and remove the baked on crud around your muff tip and you're good to go
B B