Motorcycle Repair: XR650R Jetting, honda xr650r, valve adjustment

Question
I have a Honda XR650R (keihin) that I made the mistake of doing the following all at once instead of taking my time and doing it step by step and now I'm stumped. I replaced the clutch, repacked the muffler, modified the sidpanel to allow more airflow to the airbox, replaced the air filter,re- routed the breather from the airbox to its own independent external filter, installed a FMF jet kit and did a valve adjustment. It ran perfect before my hurried build up.The clutch works great. The bike idles but bogs as soon as you hit the gas then once it reaches top end it sputters roughly with black smoke. Also the plug is black. Yes its running rich for sure. Both FMF and XR'S only(company that manufactures the side panel cut out) recommended that I run a 70 to a 75 main and the needle clip in the 3rd position. With that setup it runs extremely rich. Thats with the fuel screw all the way in too. I started at 2 turns out. There really doesn't seem to be much effect on the sound or RPM when adjusting it. I swear it seems like I have tried every combination of leaner mains,pilots,fuel screw and needle positions. I started at a 175 main,68 pilot, 3rd position on the needle and 2 turns on the fuel screw. I have worked my way down all the way down to a 145 main,65s pilot and the needle in the 1st position. When I went down in the pilot size lower rpm power improved so I have improved on the pilot circuit but as it continues through the rpm range it gets a little worse in midrange then sputters horribly from upper midrange to redline.  I also realize that the muffler packing,valve adjustment and air filter type and even the spark plug could also influence this too so I have repacked the muffler twice,replaced the plug,bought a new filter and have checked valve adjustment a million times. The deal with the valve adjustment is that it had to be tightened down .002 tighter to honda spec otherwise i would get tapping. I have tried just about everything I can think of. My bike has been sitting for months because of this and I am considering getting it dynotuned or just taking it to the local honda dealer. I'm just afraid its going to cost me a bundle. I want it done right for as cheap as I can get away with. Tuition isn't getting any cheaper. Thanks for any good advice you can lend this way.

Answer
Kendall, the engine is rich as you say.  This can be caused by too large of a jet, a restricted air filter, restricted exhaust, float level set too high.  The air screws only modify the mixture at idle and just off idle.  I'd suggest you check the float level and make sure it shutting off the fuel at the right level.  Do you have a manual to tell you how to set the floats?

Regards
Rich