The problem solving is further complicated by the fact that it runs well for an hour or two, then starts running crappy again.
saxman
If it isn't the Power Commander, it's likely fuel related.
Did you change the fuel filter after this problem started and it did not go away? Or did you install a new fuel filter before the trip?
A friend of mine just went through this exact same problem. Installed new fuel filter shortly before leaving on a trip, and ended up having to drain the tank and clean the
new fuel filter in a hotel parking lot. It was dirty, and once cleaned, the problem disappeared.
The fact that it doesn't happen when the tank is full points to two different things imho. The pump's NPSH...or net positive suction head...if there is a suction issue, the more fuel in the tank will help relieve the problem by increasing the suction head. (I work with pumps for a living...lol, I'm used to these issues;)
http://en.wikipedia.org/wiki/NPSHAlso, could be fuel tank venting. If the tank is not venting properly, you will pull a vacuum in the tank when the fuel level drops. I know it's more of an issue for gravity fed carbureted motorcycles, but it's still a possibility. You can test this by popping the fuel filler cap open when the fuel level is low, and see if you still have the same problem.
I've been around a lot of Power Commanders, and I've personally never seen one fail. Ever. I have however seen some of them cause problems due to chafed wires and/or poor grounding, which are installation issues. If I work on a bike with "issues", I always disconnect the PC first, just to rule it out.
JMTCW,
Rem
