If the fender is interfering with f. derailleur, just cut away 5mm of fender edge to give clearance. SKS rears were actually made this way for a long time.

As far as fender stay interference with disc brake, simplest thing to do is bend them around to give clearance. Not the prettiest solution, but, you'll hardly notice after a while.

Mounting fenders well can be a real challenge that may require a little resourcefulness and creativity.