Ok, so after some further testing I've revised my post. Any answers are appreciated. I am using the latest not64 as of this post and I have the following questions:
Does killer instinct always have black skies for the rest of you? (compat list doesnt mention this)
Does banjo tooie really crash in stage 3 like the compatibility list says? Making the game unbeatable?
I figured out my save issues, but for whatever reason goldeneye64, perfect dark and conkers bad fur day will create savestates but when trying to load them it locks up the emulator. Is this still a known issue?
Is there any difference in framerate from using 4:3 to 16:9 to 16:9(forced)? I cant tell.
Is there any benefit to using wii64 at this point? Not64 seems completely superior from what I can tell. Thanks in advance!