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Power Commander "BIG PROBLEM"?

Hey Guys,
I need some serious help here. This is my first Harley. I just purchased an 02 HD Ultra Classic and I know nothing about it. The bike has the 103, 6 speed trans, Rhynhart true duels, and unfortunately (according to the HD techs that currently have my bike) a Power Commander III. I took the bike in because it was intermittently powering down - lights and all. Most times I could switch the ignition off and then back on and the bike would restart. Other times I would need to let the bike sit for a few minutes before it would restart.

Harley techs Diagnosis: 1st: Gasket in Fuel tank disintegrated, clogged fuel filter and ruined fuel pump. Replaced both. 2nd: Power Commander is creating electrical problems. They do not service PC so I told them to replace it with the HD Race Tuner, they attempted to install 3 new tuners and said that the bike burned out all three, they "found" a used tuner that had been tuned to a 103, installed it and now the bike is running. They said that they had to disconnect all effect lighting on the bike (after 35 hrs of wire tracing), and that they could not and would never be able tune the bike, dyno, or access the mapping on this new (used) tuner. They told me that the PCIII caused so much damage that they did not know if the bike would quit running again in 2 miles or 10k miles. I need to go pick up the bike and I am really frustrated. Any advice would be greatly appreciated. What might have been damaged by the PCIII? Why can’t IT be fixed? Why would all of the effect lighting have to be removed? Why would they not be able to tune the new (used) tuner?
 
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I am by no means any kind of expert on this but I would find it hard to believer that a PC could create the havoc you are describing. once it is taken off the bike it would no longer have an effect on the electrical system. I would suspect that if you have an 02 with a 103 and 6 speed there has been an engine and trans swap. Though you could stroke the original 88CI up to a 103 it didn't come with it or the 6 speed. It sounds to me like a mix and match gone bad..
 
I was not able to talk with the selling dealer when it was new, and when the 103 work was said to have been done before delivery. They are out of business (FL). I was able to talk to the HD Dealer that put the 6 speed in it. They have the record of the Trans install, but no records of anything else on the bike. All numbers on the bike match up. I am not sure if this matters but, the bike only has 10k miles on it!
 
I would start by eliminating the PCIII, see if it runs without it and then checking for any DTC's.
 
HD says that the bike is running - just no longer "tunable", that the bike will not take a HD Race tuner (keeps burning them up), they cant tell me what was damaged by the PCIII, and they cant tell me if the issue is fixed. What is DTC's?
 
Yes, the PC is removed. Service told me that they put some kind of stock HD tuner on it from another bike that was a 103. They said that the bike kept "burning up" the new HD tuners. Bike IS running now but, they said its not tunable and that they really are not confident with the fix.
 
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