300ex bogging, hesitation

Ok fellow riders. Let me explain the problem in as much detail as I can.

First 1996 300ex, completely stock. At half throttle it bogs, stutters, hesitates, whatever ya wanna call it, in neutral. When riding, 1st gear allows me to go maybe 5mph, 2nd gets me 8-10, and so on so forth.
Checked plug, it was black, replaced it, same problem.
Checked fuel, noticed a lot of junk in the tank. Emptied tank, cleaned. Removed carb, tore down, cleaned, reinstalled, all stock jets, needle clip positions, everything stock. Removed fuel petcock and cleaned it. Reinstalled all with fresh gas, same problem.
Researched 14pages on another forum and found that some say to ground the neutral and reverse switches on the cdi side of the harness. Did that, same problem.
Swapped 3 known good cdi boxes, 2 reverse inhibitors, and 2 good coils, all with the problem still happening. Everything I have tried has not gotten rid of the problem.
Also just finished replacing the cam and exhaust rocker, timing is dead on, compression is great, valve lash is set at 6, all done a couple of days ago, ran great when I finished it, now today this starts.

Now my brothers 98 300ex with SuperTrapp slip-on and .50 over piston, developed the same problem at the same time. All he did was ground both switch wires and it solved his problem, so we believe, need to test ride to verify.

Both were running fantastic 2 days ago. Help me please. I just got this bike a couple of weeks ago and have not even been able to ride it. Have a trail ride planned Saturday and would love to go. Sorry for the long post, but I believe it is better to inform as much as possible to get help over the intraweb. Thanks in advance.