2006 vstar 650 loses power at around 50 mph

Your description sounds more like a torque converter clutch problem. It would explain the poor mileage, having to floor it to go. I suggest having the transmission scanned, looking at the slip speed of the torque converter clutch.

Check the throttle cable it sounds like it has come unlocked On the driver side of the carb you will see the cable going to the trans. With the air cleaner off and engine not running take the carb linkage and open the linkage wide open while doing this watch the throttle cable if the whole spring loaded housing moves then it has come unlocked. To reset the cable hold the linkage wide open and push down a black tab located on the housing. If it is already down and the housing keeps moving then the housing is striped and you will have to replace the cable assm.

IT sounds like fuel starvation has it got a vacume petrol tap if so it could be that not letting petrol through sometimes or the vacume pipe is split or kinked or squashed

Your idling jets works well, but your throttling jet may have blocked in it. open the carburator and clean it.

with black plugs it might be that there is no back pressure because of the cut off pipes. It also could be valve guides leaking oil into the cylinders.It is most likely that the carbs are not tuned to the opened exhaust

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