Each and every time you turn on the ignition, the computer compares the the home position settings to the settings it "learned" during the initialization process. The stock system and the ThunderMax keep learned settings through a "stay alive" wire that has a very low current draw. This way, it can compensate for normal wear and tear on the throttle shaft and throttle stop. If the power was interrupted and the initialization process was not re-done, the world wouldn't end. The bike would just run roughly as the IAC and TPS would be out of whack. Shutting the bike off and re-starting it enough times would eventually work its way back to where it should be; it would be more of an irritant than a major issue. You'd be thinking, WTF, it ran fine before......
As a side note, all of our throttle bodies are put on a flow bench and the blade setting is adjusted to a spec of air flow "leaking" around the closed throttle blade. The setting screw is then sealed with epoxy to discourage adjusting it as changing the blade setting alters the airflow and upsets the AFR, especially at idle and the first few degrees of throttle blade movement where the percentage of air flow increases are the greatest. Mose issues with an EFI tune-up are in this area; as the throttle opens further, it's much less of an issue. Because the TB's are calibrated in this manner, and the CNC processes we employ for porting, combustion chamber machining, piston and camshaft design are very stable and repeatable, it's pretty much the choice of exhaust systems that dictate how much tuning will need to happen after we've made the map. If the exhaust system is a match to one of the several popular staples we map to, usually very little tuning is needed.
If the exhaust is not a match (similar style but different brand), some tuning can be expected. This is where the AutoTune really shines as it will very quickly make the adjustments necessary to bring the tune-up in line. And the factory throttle bodies are not calibrated to anywhere near as tight a spec, which would explain why some guys have had great success just bolting on the ThunderMax and riding while others found it necessary to do some tuning-- the throttle body on the no-tune bike was probably quite a bit closer, blade setting-wise, to the one we mapped with than the other bike was. Again, the AutoTune can handle these differences easily.
Regarding the cable differences, I suppose the combined length of the manifold/throttle body might be a little bit longer than the stock unit due to the larger overall diameter of the unit, but I've never held them side-by-side to see. Sometimes, ya gotta do what ya gotta do to make it work; not unusual in this business. As far as the MAT sensor harness goes, I've done a fair amount of these myself and have yet to have one that was long enough to fit without the extension....but if you didn't need it, fine. But I can only imagine the wrath I'd be hearing if you did need it and didn't have it......
Glad to hear you got it together and it put a smile on you face. Did you send my cams back yet? I'm just sayin'........
Thanks, JK