AO: Nole 60 -40
RG: Fed 60 - 40 (Fed beat Nole in 2011 when he was far from his peak)
USO: 70-30 (Fed almost won in 2011 on that slow surface far from his peak)
It's much more complicated than this.
Federer is obviously weaker than the Federer of 2005 and 2006 BUT even when he was at his peak he played some really ugly matchs, even in the biggest tournaments, but more often than not, he was great.
Now it's the opposite, more often than not, he's weaker BUT sometimes he plays very very well, like this semi in the French in 2011.
I doubt you have a clear memory of Federer level of play in his peak years.
In the AO 2006 he was very average, weaker than Djokovic for sure. In the French in 2006, he was not THAT great, against Nalbandian in semis he was in a big trouble until this injury, playing like a fool and shanking his shots left and right.
Djokovic is generally much better than this. In 2007, same story, in the French he was so-so against Robredo and very average against Davydenko in the semi, the russian chocked pretty badly in this match. Overall, in 2011 he played his better "big match" in Roland Garros in term of level of play.
So, it's wrong to say "he won past his peak so in his prime he would have win easily". In the REALITY, Federer has never been stellar in the French, but the clay field was very weak. (the fall of Gaudio, Coria, Ferrero and Kuerten's injury didn't help) Proof of that, the fact he managed to be in the final in 2008 despite playing horrible in the whole tournament.
I think that "Jesus-Fed" is better than Djokovic by a fair margin, but in slams, Jesus-Fed wasn't there eveytimes, even in his golden years. Djokovic would definitely have beaten him a few times, for sure.