Duane, sorry to hear about the chimpanzees who worked on your bike. I started a thread on this general topic about 6 months ago, relating to whether it's worth the hassle to bring a bike into a dealer because of the risk of, or perhaps the inevitable, collateral damage, even if they're able to fix the problem. I service my bike myself just for that reason, and if it ever needed major work, I'd much rather pay Jim (HD-Dude) who is local to me, to either do it for me or with me. Unfortunately, the guys (like Jim) who really know what they're doing and have the experience, patience and skill to both fix the problem and not screw something else up in the process generally don't work at the dealers, so--no warranty benefits.
I'm sure you know this anyway, but when you talk to the HD service rep, if he asks you to sign anything (like a release), tell him to go pound sand. I don't think they'd be dumb enough to try to void your remaining warranty after the fact, and they pretty much lost any leverage once you picked up your bike, right? (Yeah, I'm a lawyer, but please don't hold that against me--this is just friendly, as opposed to legal, advice.)
Idiots. Makes me sick.