I think that Federer would have a winning h2h against Muster on clay.
We all know that even on clay Muster had a very poor set of h2hs against serve-volleyers, but he could struggle against strong attacking baseline games on the surface as well.
Stylistically the most similar player to Federer from the 90s was Michael Stich, who had a 2-2 record against Muster on clay, winning their most important match at RG in 1996. In that 1996 match, Stich didn't serve volley that much at all, and stayed back a lot and attacked from the baseline, and that threw Muster off his game.
I think that Federer's attacking baseline game and occasionally forays to the net would cause Muster a lot of problems.
Now Sergi Bruguera and his vicious topspin would cause Federer a lot of problems on clay I think.