its Super mario 64 (Usa) so i guess its NTSC ? Pal is Europe right?

Only thing I can think of is the timer

If you have the timer on at all times it causes lag

But wouldnt that make my rollouts etc worse in the usamune and not vice versa?

Only thing I can think of is if (assuming you're on EMU) your ROM settings are different from the usamune rom to the sm64 rom

i just checked those and i had some different settings but it seems it doesnt fix the problem https://imgur.com/a/1T8iFe1 ( leftside is SM64 settings right side is Usamune )

What both of the above said, that or "stage fright"; I play worse when it matters too, but I know it's just nerves.

I was not even doing runs just testing it out outside the castle and in some stages without some actual timer running and the game feels different somehow

Is There any difference between those 2 other then the extra training settings? I Spent like 99% of the time i play sm64 in the Usamune and alot of the movements seems fine but once i switch over to the normal Rom simple stuff like rollouts , double/triple jumps are hard to execute.

Is the normal sm64 Rom more lagging or is there any other reason why this keeps happening