that is a strange problem you have there.
here is a good gear ratio calculator i use alot:
http://www.grimmjeeper.com/gears.htmlreally helps put the numbers you posted up above into a more comparative format.
personally i would pull your rear third and count the teeth on the pinion and ring gear. any time you have a consistent ratio difference like you have there it would lead to one torque multiplier being different than the control (the stock setup in this situation). I could see if someone put 5.29's or 5.71's it would be close to the amount off you are seeing.
glad to hear you checked the MPH and RPM with an external source too to eliminate that cause.
also, it cant be in low range or you would not get to 65 even in 5th at 4k rpm, the low range would put it over 200% off.
