Has any one ran a Alternator with a internal voltage regulator?

Thank you for you time on helping me. this problem is giving me a huge headache not the greatest when it comes to electrical. so i will start from the beginning maybe you will think of some thing i couldn't see. So this problem all started last year when i refinished my dash then put it back tho together. not sure why maybe a wire got screwed up in the processes but i don't think so never changed any thing still have everything grounded. ive been trying to figure the problem out but coming up with nothing. ive checked all the grounds ive replaced voltage reg. also i run a voltage gauge. not sure what to do next i plan to do re wiring of the alt do i still run the output wire on my volt gauge? also parts store said alt was good im running out of ideas please help
thankyou nate baluski