The header thing does suck! Before I changed mine out, I got used to just loosening the screws and lifting up out of the way of the oil filter.
Of course, you have to take the exhaust
off first. Eventually, I put the White Brothers
header and E-Series pipe on which solved the problem(other after market exhaust systems will accomplish the same thing). I also installed the Terry Hot Start system. AWSOME! It allows you to engage the hot start choke without having to reach down and find it. This is really usefull in awkward positions when it isn't convienient to take your hands off the bars or, if you install a larger gas tank that hangs down further and obstructs access to it. The jetting issues don't apply to you. I had the same experience. With stock jetting my bike ran fine from sea level to at least 6500 feet. It was a little rich though. Eventually, I changed over to YZ timing. I took it into the shop where they have the dyno and smog stuff. Wound up just making slight adjustments to the jetting. Like you said my bike just plain rips. Having said that, some of the guys on this forum are real technocrats. They want to squeeze every ounce of whatever they can get out of these bikes. So they tinker. Sometimes with great success. Its all to complicated for me too!
Hope this helps a little. P