Going through Stone Tower Temple with the Kokiri Sword is gunna be a pain in the butt. You really need the Gilded Sword if you want to beat Gomess and Twinmold fast. I attempted both with the Kokiri Sword and it took a really long time.
I never had any problems with freezing with the N64 version unless I pulled the cord too much which could happen to anyone. One time it froze on me when I was moving the N64 in another spot but the game was fine. It seems to run fine on a fast computer through emulators but with a slow computer like mine, you never know. The Gamecube version is the worst for me. I don't know if the disc is really scratched but it's locked up on me so many times, it's really annoying.
Lastly, I got a hacked Majora's Mask on my Wii and out of what I've played, it hasn't locked up on me at all which is a good sign.