Jenna, you mentioned that Wheatley "locks" their tunes. Nelson does so as well, even though they sometimes claim they don't. I installed a remote starter on a friends truck with a Nelson tune, and the factory anti-theft system bypass module would not work for some reason. It would NOT allow the engine to start without the key. After a few days of research (and many headaches) we confirmed that the bypass module was not working because it basically tells the computer to bypass the Passlock system and allow the engine to start. But with the ECM "locked", that wasn't allowing the module to communicate the bypass signals to the ECM. And Nelson was zero help. They just kept insisting that they automatically bypass the "VATS" (even though it's not even called VATS on our trucks) when they do a tune. They were basically making all kinds of excuses as to why the tune could no way he responsible for the problem I was having. Just to prove to my friend that I knew what I was talking about, I purchased another bypass module and we had the same result. I then tried both bypass modules on my own truck (which is BB tuned) and each allowed my remote start to work properly (after being programmed to my truck if course).
Bottom line, I went old school with it and did a hardware resistor bypass at the ignition switch instead if using the databus wire bypass module and then that allows his remote start to work just fine. And reason being is because there is no "communication" with the ECM, the resistors just fool the ECM into thinking there is a key in the ignition.