Don't know if any of you have tried this, but I read a thread on another site. A guy running a PCIII recommended that after you get you bike to where you want it, have the stock ECU flashed by Harley with the closest flash to your build, then add the PCIII back and get your final tune on this setup. That way if you did ever have a problem with the PCIII, being a piggyback system, you could just unplug it and would be in the ballpark with the stock ECU to get you home. Sounds good to me, if you can get a flash that is close to what your running.
Talon,
That is the method many of us with just stage 1 mods use, get the H-D stage 1 calibration first, then add the PC. The problem comes when you do major mods that have no corresponding H-D calibration. You can still run (poorly) with the stock calibration, but depending on your mods you probably wouldn't want to go very far to prevent damaging your engine.
Before people go crazy over worrying about this stuff, you need to understand that the average failure rate for electronic boxes like ECM's, PC's, etc. is very, very low. As in less than 1%. And I definitely wouldn't let the "possibility" of a failure keep me from choosing a PC. Carry your map on disk or flash drive at all times. If you have a rare PC failure, buy another one and load your map. PC's can be found in lots of places all over the country, and most shops and dealerships have the software. Or for that matter, as cheap as flash drives are you could load the entire program on it as well as your map and then just keep it somewhere on the bike.
I don't think I would let certain dealers unwillingness/inability to work on aftermarket tuning devices keep me from using the device I want. And I sure wouldn't let them force me into overpaying for a SERT if that wasn't my first choice of tuning device. The issue in the first post of this thread isn't necessarily a problem with the choice of aftermarket tuning device; it sounds more to me like a dealership with no diagnostic talent using it as an excuse. The same place may very well have been unable to diagnose the problem even if it occurred on a totally stock bike.
Jerry