Muster is my all-time favorite, but these types of "What if" scenarios, while fun to think about, are really impossible to gauge. Certainly, Muster could've benefited from today's string technology. With that said, my feeling has always been that Nadal does everything Muster did, but better. I'm not really able to judge how adversely Nadal's game would be affected by having to use the 1990s strings.
I think the fitness/stamina category is the only area where Muster may actually edge Nadal. Muster moved well, but Nadal moves better and is way more adept at transitioning from defense to offense within a point. Like Nadal, Muster liked to dominate rallies with his forehand from the middle of the court and force the other player to do more running. Neither was known for his serve, but Nadal's is probably a little more effective. The interesting part of this fictional matchup would be the lefty vs. lefty factor.
In this totally fictional matchup, I feel like the Muster from 1995-96 (on clay) would hold his own for sure, but I don't think he would have enough in his game to consistently trouble Nadal.