something is not right..that motor should rip. i can tell you that jeffs motors run strong, so im gonna say that a problem on his end is not happening. also, you should be running those 35's. 28's are NOT enough carb for that 4mm motor, or any 4mm motor for that matter. how did you check the difference in power between 2 bikes? ride one then jump on the other? or did you drga race them? ill guarantee you that your 4mm will flat out spank any stock stroke, stock port banshee.
your jetting in the 35's should be right around 160 main and 45 pilot. what air filter setup are you using by the way?
if you have a problem, you know you can always call jeff. he built your motor and would be happy to give you some insight on what thew problem is..
whats your timing set at?