1996 cbr f3
R/R is from yamaha R6

Ok, I tried going out for a ride yesterday, Tried starting my bike, but it looked like battery was dead, i went and bought a new battery but the light on a dash were still dim and it wouldn't start unless jumped from the car. after jumping it the charging system was working properly (about 14 V at 5k rpm), however it shut off on me 3 miles down the road, At that point the light were much brighter and it even cranked a little, 5 min later started by rolling down the hill, on the way back it would work fine in the low rpms (up to 3500) but if tried to take off it would feel and sound like only works on 3 cylinders. When i got back and checked voltage it would have around 13.5 V at 2-3 k rpms but would drop to 10 V if revved higher.

Also the starters positive terminal if checked by multimeter seemed to be shorted to the ground (not sure how much resistance is actually suppose to be there)

Another thing it looked like when hitting the start button the light on the dash will actually become brighter.

 

It sounds like you're having electrical problems and the first place I'd look is the wiring for that R/R to make sure something didn't come loose or is getting grounded. Many people including myself use R/R's from other manufacturers. There is nothing wrong with that, but since it's not just plug and play and what you're describing seems to relate to that, it's where I'd start.

As for the check you made on the + terminal of the starter, that would be normal. There is very low resistance through the windings of the starter, and that's what your seeing when you check from there to ground. That low resistance is what allows the starter to draw large amounts of current to start the engine. Nothing to worry about.