So I was hoping to get into this game since I used to run LADX and tried making a premade file and then making a copy of it to compare against runs and the grunt sounds at the beginning are different everytime. I know that the manipulation would try to listen to the grunts Link makes at the beginning but am now confused if they even matter now if I've made a copy of the same file or if I'm making the pre-madd file wrong

The grunts Link makes are determined by the same RNG that determines the Egg path (and the D4 tile puzzle order), but ONLY after you make the file for the first time. For now, listening to the grunts is simply a way to help determine that your manipulation was successful.

Using that same file as a premade file for runs thereafter will result in different grunt sounds, but the same exact Egg path and D4 puzzle patterns, so you don't have to worry about that.

In other words, no the grunts don't matter as long as you keep using that same pre-made file.