Bike will start to misfire and hesitate if battery is dying or the voltage regulator is bad or both.
Sounds like the tune may be having a problem once the bike warms up, and goes to the next step in the map, something is missing or goofed up in the map. Have you cleared the TTS back to stock to see if it does the same thing? Try loading the current map again, or pick another map and try it. Make sure you have a fully charged battery when installing the map, or it will not load properly and cause some of the symptoms you are experiencing.
Also, the Fullsak setup like many others open pipe systems kill the low end driveability and torque. May have to dynotune to get the hesitation out. You also need back pressure for low end smoothness and driveability, like Supertrapp Mufflers provide.
The mechanic fully charged the battery and checked the charging system and said all was OK, he also checked the VR to see if it was affected by the recall.
My current map is one I got from Steve at Fullsac and has been on the bike without issue for about 1500 miles, the map prior to this one had some decel pop. I have not gone through the V-Tune process. The mechanic is suggesting that maybe I put the factory tune in as well if the throttle position sensor does not work. I am not sure what to expect with the stock tune with a header pipe and 2" baffles, how will it run or will it even run??? If in fact the TPS does not work out, I will do as you suggest and try the previous tune I got from Fullsac. Is it even possible that a tune can get goofed up, in my simple mind I can't see how that can happen???
I suppose I shot myself in the foot by not doing the VTUNE, now this is an unknown varible that may or may not be affecting drivability???
I did learn something interesting though. The mechanic told me they cannot tune a US bike or hook up some special tool that they use to tune with. There are only certain dealers here in Germany with the ability to tune US bikes. That being said, they cannot determine if I have retuned the bike so for routine maintenance they will not flag my bike at this dealer. Problem lies if there is something more serious with the bike and they need to send it to the other dealer.