If you want to be conservative, Federer would have a minimum of 3 RG titles without Nadal.
My guess is that he'd have at least 4 and probably five.
Be conservative an say Fed only wins 2 in the span of 2005-08, losing twice to Djokovic or whatever combination you want to use. That is two. He won 2009 outright and beat Djokovic and lost to Nadal in 2011, so it is a stretch to not give him that.
My guess is Federer wins 2005. I'll say from 2006-08, Federer gets two and Djoker gets win. Fed wins 2009. Fed wins 2011.
The fact is as far as a sustained level of excellence on clay over a period of consecutive years, Federer's clay performance from 2005-09 is probably as good as anyone over a 5 year stretch outside of the two clay GOAT's, Nadal and Borg.
In that span (2005-09), Federer played in 19 clay court tournaments during the run-up to Roland Garros from April until the slam.
Here are his stats:
Overall Record: 83-14
5 Wins (Roland Garros, Madrid, Hamburg x2, Estoril)
13 Finals (Monte Carlo x3, Hamburg x3, Rome, Madrid x2, Roland Garros x4, Estoril)
15 SF (add 1 to Roland Garros and Rome on the above list)
17 QF
14 Losses - Nadal x9 and one each to Djokovic, Gasquet, Wawrinka, Volandri and Stepanek