Federer was only affected by the adverse effects of mononucleosis the first 2-3 months of 2008. Apart from that, he was equally good the rest of 2008 and 2009 than in 2004-2007. In fact, only in 2009 did Federer win RG. According to this New York Times' article doctors said Federer was recovered from the adverse effects of mononucleosis as soon as late February. He received medical clearance to play normally the 27th of February 2008. Reference:
http://www.nytimes.com/2008/03/07/sports/07iht-arena.3.10811374.html?pagewanted=all
Federer arrived to the Wimbledon final in July (more than 4 months after the medical clearance). Federer was moving perfectly in Wimbledon 2008, and he arrived to the final without losing any set. He was 26 and didn't look less fast than in 2007. So he was at his peak. Even the 2007 final was kinda close, Nadal had 4 break points in the 5th set. 26 years old Roger was 100% healthy and at his peak in the 2008 Wimbledon final.