How to fix custom song glitches on emlators.

Test them how? You mean like see if using them can produce glitches in songs, like having it up to the max of 3700 and then adding them into the song data as well?

Yes.

But no I haven't, all I know is they are more or less basically built into the sound engine.

I'm pretty sure they are taken from somewhere in the ROM and aren't build in the SPC-700 or DSP but I'm not sure where they come from...