Technical Problem w/Fuel Injection or Incompetence

In late June of this year I took my 2000 Monster 900 to a local Ducati dealer for it's 12,000 mile tuneup. Shortly thereafter I took it out on a long road trip and found that it was losing power at altitudes above 2000 feet. By the time I made it to my destination at 3500 feet I had to run it with the choke on just to keep it moving. A local technician did a quick and dirty adjustment to get me back over the mountains, and I then took the bike back to the original shop. They put a few hours into it (no charge), and somehow managed to make the bike run worse. Now at sea level the bike was dying at stoplights without the choke or constant blipping of the throttle.

At this point (early August) the service manager was convinced that it was an electrical problem, and kept the bike for a week and a half swapping out electrical parts, but without finding anything wrong. Finally he swapped out the stock ECU and installed a used Ducati Performance ECU. Now it at least has power when you ask for it, but after it gets warmed up it still starts dying at stoplights and the engine sounds like ****; extremely gravelly and unsteady.

Now, with summer over, I've got an appointment with a different shop and I'm trying to talk to the factory zone rep. So my question, does this sound like an actual technical problem with the bike or is the guy just incompetent? Am I justified in demanding a refund from the first shop?

thanks,
fever