I have the gel seat but on long trips I use a sheepskin, helps a lot. For pegs I went to Knightsdesign lowered pegs for the fz1, huge difference and great poeple to deal with.
Yamaha Aftermarket Parts - Knight Design - FZ1 Footpegs
I am 6 ft 2 with bad knees, I purchased the one inch lowered pegs from Knightdesign, I am now comfortable for extended periods. These are very well made and simple bolt on. The fz6 pins work also as you must drill out the stock fz1 pins...