Welcome! I'm new here myself. I have the same bike you do, and came off of an '04 R1.
You're Triple must have been a lemon - my experience with Triumph QC is that they have improved tremendously. With all the problmes you experienced, it just screams 'HANGOVER' on the assembly line
I owned a 2000 Sprint ST for a while and some days I wish I still had it. Never a single issue; it was as reliable as my Japanse bikes, and it had that sweet triple engine. It was also great on gas - I'm guessing either the new 1150 is a bit of a pig, or (more likely) there were even more problems with the bike that you hadn't even found yet. The fouling and the mapping problems lead me to belive the latter.
I can certainly understand your predicament, and you're smart for getting out from under the S3 while the getting was good. Its a fabulous looking bike, but its one of the most impractical bikes ever conceived. I think even my R1 was more practical in many ways, and thats saying something. The S3 was actually a bike I contemplated, but lack of luggage space, the fact that they bumped the displacement (insurance problem for me at least...), and the fact that it wouldn't have slowed me down at all kind of sealed the deal. I wanted something simple and low maintenance, but still a blast to ride. I got my wish, and it cost about half as much.
That being said, if I had a few bikes in the garage, an S3 (properly sorted) would likely be one of them