Yea, that's exactly what I was thinking. I see it running hotter and thought it must have leaned out the mixture because of better ignition. Unfortunately for me, that hypothesis turned out to be false as the mixture was dead-on what it's supposed to be.
Interestingly, many of the parts and approaches used on the K100RS match what are done on the same vintage BMW E30 cars (3-series). Yun Lung Yang
posited that the coolant temperature sender that feeds temperature info to the ECU is likely bad. Apparently, the ones in the cars have about a 15 year life span and then they get flaky. Symptoms of this are that the engine takes longer to heat up and once it does it tends to run hotter than normal. I found a thread on a K100 site that seems to support this hypothesis.
So on Friday I'll get a replacement sender and install it to see if that resolves the issue.
I can say that the bike is run significantly better in all aspects other than temperature. It's a fun bike again, and it wasn't running badly before at all (with the exception of the occasional cylinder dropping out issue which was the original reason for changing the ICU.)
As for an engine transplant that's really not feasible. This bike doesn't really have a frame. The engine and transmission make up the bulk of the frame. There's really only a piece bolted to the front that supports the fairing and steering head and a section bolted onto the back for the seat and cowling.
Realistically I should be able to run the bike for quite a number more years. I suspect I'll run into more electrical and electronics issues since we're getting towards the expected life span of those components. In addition, seals and whatnot will start failing. The rear main seal has started seep leaking, for instance.
But it's still a great bike for me and I'm no where near ready or willing to exchange it for something else. It's my bike after all. No other bike will do.