This has got to be a joke? Federer is a 1 time rg champion and 4 TIME FINALIST.
He would EASILY win several (i am betting 3-4) rg's in any other era. Nadal was his problem... not clay.
Here is your basic problem. You are equating what he has done within his particular era and transporting it back to the 90s. You can't do that, time travel doesn't work like that, so don't cherrypick.
Once you work that out, then you have to look at the respective games of the players who played on clay in the 90s at that time. Guga on one good hip beat him, you think he couldn't do it at his peak? Bruguera would be breaking Fed's backhand down like he did with Sampras and unlike Muster he loved playing passing shots.
In other words the clay games that trouble Federer are were more widespread then than now, it's much different on clay with Kuerten, Muster, Bruguera, Medvedev, Corretja etc. Even allowing this Federer wouldn't play the same way then as he does now, it's that simple.