If stock sensors would fit in there OK, I don't look for Rinehart to be real sympathetic. After all, that was the story they gave on the brake pedal.
Got to agree with Brian. If the stock parts would have fit that's where their responsibility ends. It's not Zippers job to make sure their parts work with Bub's pipes. It's not Bub's job to make sure their parts work with Zipper's aftermarket stuff. The OE configuration is their template. Anything beyond that is up to us. Any help they give above and beyond stock configurations to accommodate other third party parts is to be appreciated and applauded. But it can hardly be expected.
Granted, after things have been on the market for awhile and everyone sees everyone elses stuff those things they see more commonly will also get accounted for and adjusted to. But that takes time. The T-Max's autotune package is new stuff. Bub nor V&H nor likely anyone else is building their pipes with Zippers in mind; they've been humping it to do with Harley in mind since the 07 product releases.
I personally can't fault the vendors on this one. They can't know what we've got, what we've changed or be expected to account for all of our changes. This stuff is as much (or more) art as it is science sometimes. Making thing play together is just part of the task.
C.O., it's not my position to suggest what you'll feel most comfortable doing or what you might think is fair. Were it my own bike, however, I'd just fix the damned thing at this point. The fix is, after all, a simple one.
The pipe has to come on and off at least once more no matter what you do. If you send it off for replacemet you're down time, shipping costs and likely a couple weeks frustration waiting for stuff that still might or might not be just what you need when you get it home. Alternatively the pipe could come off after breakfast some Saturday, you could haul it in town to a muffler shop, leave it with him while you get a sandwich, come back right after lunch and put the bike back together that afternoon and ride it to dinner that night. Total expense won't be but a tiny bit more than the freight cost doing it the other way. And you don't have to worry about it or fight the problem anymore. Sometimes it really is best to just declare victory and move on.