I also have the factory Nav system and I upgraded the speakers the first week I had my Hybrid. I used Boston Accoustics FS80 Component Speakers in the front and Boston Accoustics FX8s in the rear. These are a marked improvement over the relative junk that Ford supplied. While I had the door panels off I also installed Dynamat Extreme. I encountered no real issues during the install. I mounted the Boston tweeters in the factory sail panels using brackets. The new crossovers mounted in the doors, well in front of the windows...there is plenty of room. Very pleased with the results.

2006 FEH 4WD Dark Shadow Gray