Motorcycle Repair: rough running 05 eletraglide fuel injected, air fuel mixture, vibs

Question
Back in April I took my bike in for 30000 service. When I got it back it ran rough. Took back and told that everything checked out ok. Still running rough and called customer service in Milwaukee. Took bike to dealer I bought bike from and got it back and was told eerything fine and was my imagination. Mike I've been on bikes 40+ years. I cant believe its me. I took to independent who said there is definatly a problem.He wont work on it because he says if Harley with its database cant figure it out then he isnt equipted to repair. The dealer charged me $304 and said they checked runout and compensator and replaced cam cover gasket. According to Independent they couldnt do that work for that much. What could have changed from when I took a good running bike in for oil and plugs to a bike that developed a primary leak and cracked both fairing mounts in two months? I'm not a mecaneck but I know a few things about bikes. Two dealers in my area have both said theres nothing wrong with my scoot. When its running between 1000 to 2000 rpm it runs real rough, enough to shake my eyeballs and slide my feet off floorboards. It seems to smooth out after 2000 rpm but I still feel some vibs. I was planning on taking to another dealer cause I figure maybe 3 times a charm. Could they have possibly swiched the leads to my fuel injectors? Would this cause it to run rough at lower rpms?

Answer
If you changed the fuel injector leads around it would not run. As to what they did you make your bike run bad, that I cant tell you since I didnt see their work or know what they really did.
I would start by having somebody run a diagnosic on the bike and see if there are any codes showing up. If not then you need to check the air/fuel mixture see if the bike is either running to rich or to lean in the RPM range that you are having trouble in.

Good luck and happy riding
Mike