Was the clutch assembly replaced during all this? If so was the flywheel turned? If so, how much was turned off of it?

Yea forgot to mention brand new clutch, i dont know what spinning the flywheel is for, i dont think i did that.

If you don't turn the flywheel when replacing clutch assembly you will have the issue you are having now. Think of it like having warped brake rotors and just doing a brake pad slap and not turning the rotors or replacing them. The pads won't make contact evenly. Same with a clutch

Would it help is i adjust the master nuts behind the clutch pedal? Or can it run fine any other way without removing the trans again??

Yes, you can try a pedal adjustment. It may work, may not

Do i have to remove the master entirely to adjust it or i can just do it under the pedal by removing the pin?

I believe that you can do it with out removing the master