Wow, this thread went to hell quickly. Sorry Markxb9, heres some help.
This a screenshot of the factory manual for a 2006 XB:
Screen Shot 2019-04-25 at 10.25.14 AM.jpg
Are you doing EXACTLY this procedure?
If you are doing that, and getting the correct TPS angle reading at idle afterwards you can safely move on if the TPS sweep is good when tested when the bike is running poorly. i.e. pull over and immediately check it.
I am intrigued to why you get different lengths of time before it starts running poorly, but if your timing is accurate... it's a clue.
Buell cold-start programming is very rich and very long. I wonder if you have a big air leak somewhere that the cold-enrichment cycle is masking?
Go ahead and check the AFV value for another clue, and test for an intake leak. If it's not that, we'll have to stop guessing and jumping around, and do some actual real diagnosis.