Polar-Bus, doesn't your bike have a moose reed spacer (and a flywheel weight, which only testing could determine how this could affect top speed)? Although some claim reed spacers make more low end to mid range power, don't they hurt power on the top end? Have you tried new stock reeds and removing the spacer (and of course, rejet the bike for these new changes) to see if this improves/hurts top end? Do you have perfect compression?
When the KX500 was being raced by Team Green that last few years (they were still desert raced in 2005), Varner Motorsports built the engines. So, I'm not sure how many internal modifications were made to my motor, but I find it very interesting that Team Green, which had the knowledge and the resources to extensively test the KX500, refrained from installing reed spacers and trick reeds.
Here's an example I like to think about when it comes to aftermarket parts:
Look at the exhaust on Destry Abbott's 2004 KX500. It's interesting that it doesn't have a FMF silencer/spark arrestor on it, yet he was sponsored by FMF and he had a FMF Gnarly desert pipe. He has the stock silencer trimmed by 3 inches and a sparky welded on the end. Team Green claimed no power loss with this set up, and a scientific analysis (maybe a dynomometer) was probably performed to reach this determination. My FMF silencer (Unfortunately, Team Green didn't have this set up on the Brian Brown bike I bought) looks pretty restrictive with bend in it and turbine in the exhaust path, but I have no way of testing the power of one silencer to the next. All I know was on race day, this is what the factory team had on Destry's bike, so I'm inclined to take advantage of their research, and follow their recipe.