My bike is just uncorked with stock header and stock can. I also pulled the snorkel in the airbox... that mod as far as I can tell did not change much for me. I jetted my bike a year ago and have forgotten most of what I did... but PM me or use the forum if you want any other jetting info...
YamahaSteve, I have an 04WR450 and ride at the same altitude (4700' in Utah),
I was noticing your jetting settings in your signature. Do you have it piped also or just unplugged? Concerning the grey wire, is there a time when you think it's better to have the WR timing? Like making it easier to start or a type of terrain that you would want slower timing?
As far as the timing goes... I would say no. You can always use more power... just don't turn the throttle so far is you need less ... my WR still has great predictablity, meaning it has no hit... just pure smooth pull all the time... if the timing charts I were refferring to earlier were accurate (and I wish I could find them again) then the WR timing drops to zero degrees after 3 or 4 thousand RPM... this is not optimal... the YZ plot showed about 30+ degrees advance at 9k... the WR had 0 with the greay wire intact.... granted it was along time ago I saw these plaots, but I remember the zero advance aspect clearly. What that means with zero advance is that the piston hits TDC and starts downward at the same time the spark is ignited... when the engine is at high rpm the piston can outrun the flamefront which causes power loss... the advance starts the flamefront earlier so that it is pressing on the piston maximally as it starts is downward motion... my 2 cents.
edit: This has NOTHING to do with the valve/cam timing BTW... only spark advance.