I tried over clocking retroarch and it did not work, still video stuttering when loading up Pokemon Stadium 2, i also tried Lakka, still same issues, very very strange.
thanks for your reply, I've tried those options, if someone perhaps could test pokemon stadium 2 and Mario kart to see if they get any video stuttering I suppose.
As an update nothing has worked sadly, I've tried everyone suggestions and just hasnt worked at all. Pokemon stadium 2 has video stuttering, test mario kart as well and I still get video stuttering both drop the audio as well when video stuttering.
As this point, heck if someone could solve the issue i'd pay them because this is getting so frustrating, 90% of the reason I hacked the switch was to play n64 games.
I appreciate everyone's help so far, just can't seem to find any solution.