Hey mate, when you say it wouldn't turn over do you mean the engine wouldn't turn over or that it just wouldn't start?
Cool so the engine was turning over just not starting, do you know what they replaced exactly? Spark plugs obviously but injectors? Were they replaced or cleaned? The fuel pump, was it the whole shebang or just the pump? There are a few things that cause issues like this. Could be electrical.
Not sure if intake manifold seals were replaced but it sounds like my old Ultra. When I bought her she had been sitting for a while, intake seals were buggered from sitting for so long. Replaced those and she ran like a swiss watch. Plus I wouldn't be taking it back to that shop. Find somebody else if you can.
For a bike that's been down awhile all those things they did would need doing, surprised the battery was still serviceable to be honest, the tyres could be iffy, what I'm saying is it looks like they did the things that would need doing although I disagree with their sentiment towards Harleys in general, your bike is a pup K's wise, sporties run for 200k easy if they are looked after.
I'm not defending them, there definitely should of been some consultation I'm just trying to make you feel a bit better about it.
Won't be the higher octane fuel in the short time you seem to have been running it. That can reputably cause plug fouling eventually but I've never had it. With the tiny tank you just pick different fuel next time you fill.
my dyna is running about 10.2-1 comp and hates 98 fuel with backfiring and bogs down and just about stalls but loves the 95.I think a stock xr 1200 is running lower compression than that so id start with fuel.
Dodgy lead maybe, but, this happened to me, corrosion of the coil post where the sparkplug lead goes, worth looking mate, TPS should be ok, it really should but I think they do throw a code.