Are you sure it's not the mod that's causing the freeze? Because I've had a broken disc drive before, and all it did was change the screen to white background and green text, saying something along the lines of "Please Insert Disc"; I'm highly certain that a scratched disc would yield that same effect, so I'm over 95% sure that your problem is, in fact, the mod, and not the actual disc. To test it, you can try removing your SD card and play normal Brawl, and see if it still plays with intermintent freezing or beeping at all.
I tried all of this, when selecting Captain Falcon on the CSS it freezes, The Mod I was using was PM, and the disk is also cracked in a few places.
In any case since posting this my Brawl disk has completely cracked in half
so now there's no possible way to fix using it with the disk.