As a matter of principal, I will not offer assistance or advice to anyone here who messes with the welded up/painted shut, “sacred screw” on the throttle stop plate.
If someone wants to be supremely stupid, even after I have given complete information as to precisely why you don’t mess with it, then I don’t want any part of their madness.
I wish mine was welded so it would at least deter anyone from playing with it. I have always been a "by the book" guy. If the manual says don't touch then I don't touch.
I managed to get the stepper off before leaving this morning (about 4AM) and to my surprise it checked out exactly as yours did. No short to the case and no short between windings. Pins 1 and 4 had continuity with 50 ohms. Pins 2 and 3 had continuity with the same 50 ohms. Additionally the stepper was clean. I then checked the connector on the loom and found pins 2 and 3 were short to ground. Correct me if I am wrong but that can't be right. There must be a short in the loom. I started pulling plastics from around the tank, and then had to head south out of town. I didn't notice anything suspicious in the portion of the loom that I could see but here's the thing;
1) The bike has no real miles on it. < 10,000 miles so abrasion from normal wear on the loom seems unlikely.
2) The 2 shops that worked on the bike were horrible and had no idea of what they were doing. In addition to the taped up spark plug cap, I found missing washers, stripped/missing screws, hoses routed improperly and burning where rubbing on the exhaust etc.
3) The last guy pulled the right fairing away from the tank leaving the front of the fairing attached and squeezed in between the tank and the fairing to replace the oil pressure switch.
4) I know from experience in my profession that when a problem arises you consider any recent changes in routine to point you in the right direction. i.e. whenever we had a sudden drop in pressure in the City water main system the first place we would look is where a contractor was excavating. 70% of the time we would find a contractor scratching his head standing next to a hole full of water after digging into our water main.
Considering these points I have to think it is very likely this short was induced by something the last shop did. That said unless you have a better suggestion I'll finish pulling the tank this weekend and start looking in the same area where he was working.