I missed the '03 PDP and bought a '02 FZ-1 to ride while I waited for the '04 PDP and delivery. 14k in 10 months, with lots of touring type riding along with local rides. I also rode with a bunch of FJR guys for some trips, and can tell you some things I noticed. Might not be an issue for you, or might help you figure out if you want to do the trade.
Gears - The FZ is a six speed close ratio box. You row though the gears a lot compared to the FJR.
Wind screen, even with the large givi screen, the FZ is still pretty lacking in protection in less than perfect weather. Don't get me wrong, it's awesome on sunny, warm days. In the rain, not so much.
Bags - what bags!? I used soft luggage for the FZ and it did the job, but wasn't weather proof, held less, and was generally more of a PITA on trips. Can't leave it on the bike overnight like you can the hard bags. Have to always dig for stuff, doesn't hold a helmet, etc. IF you even think about putting Givi luggage on a FZ, just keep the FJR, it rides better loaded than an over loaded FZ ever will.
Seat - Well, that's a toss up. The FZ took about 4k to break in, then actually felt pretty good up to about 700 miles. The FJR seat took 6k to break in, and still wasn't great for more than 600 mile days. I upgraded to a Russell and won't ever go back on the FJR.
Twisties - here the FZ has the edge. The FJR is more stable, but the FZ is simply more tossable. You can hammer on the tight stuff easier than on the FJR, and lean waaaay over before you scrape pegs, even stock suspension to stock suspension. The longer wheel base of the FJR is better for fast sweepers and damn good in tight stuff, but you work a little harder. The short wheelbase of the FZ lets you toss it back and forth more easily, and you're still upright enough to not feel like you're back is a pretzel at the end of the day, (gen I).
HTH,