2006 vstar 650. it cranks and idles great, but when I put it in gear and take off why is it sputtering and won't exceed 50 mph?

transmission clutches bad for third gear operation. needs trans overhaul..

Probably you did not need to replace those, are both cylinders running?
was the motorcycle sitting for any length of time?
make sure the carb low speed jets are clear use carb cleaner the can with the with the tube and make sure the low speed jet will flow the fuid through it. if its clogged take a strand of copper wire and clear them.

It sounds like a cam Or crank sensor problem (which controls the coils) I can only advise u from here to find a new CAR GUY. Good luck

idle cable out of adjustment and or throttle cable needs adjusting also and they always need to be lubed at 5000 miles adjust throttle cable with wheel striaght forward idle cable to all the way right lock and 2-3mm free play on throttle grip

have you checked the carb for dirt ?
sounds like the carb is dirty and or the idle screw has moved

this symptom resembles an intake leak. Check to see if your intake seals are not leaking

What gear ratio does it have? Especially a baja set up has low gears and won't do 50 - 60 no matter how hard you push it. That is most assuredly the problem.

first thing is the engine light on?
these cars had problems with the on plug ign coils and if this is a misfire the comp will tell you which cyl is the problem.