I worked on Techline for an auto manufacturer and our first advice was always remove the aftermarket mods and retest. Here there is one thing that I might try prior to that though. You've said the only thing that I've ever had as an issue is I need to let the bike warm up completely. Your other statement is that the only thing you've changed is a switch to Waterwetter, a product known for making bikes run cooler. I'd probably dump that out and try running standard coolant so that it runs a bit hotter.

This is something to try although I agree with most other suggestions that something is wrong with your mapping, even if it worked before, computers and sensors fail. My commodore 64 used to work too.