James - From your profile it appears you have an '05. Sorry, no adjustment there. One of the changes as the FJR went from Gen I to Gen II in '06 was that the seat became a three position adjustable set-up. '03-05, (and '01/'02 EU bikes too), have no seat height adjustment.<snip> I didn't even know you could lower the seat and if my seat is in fact in the lowest position. Would someone enlighten me as to how this is done? If the seat can be lowered even a little bit it would be that much more comfortable.
There is a lot of other good advice and tips in this thread that do apply to your situation though. I would suggest seat work is #1 and has the least down sides, unless you like tall boots anyway. Generally seat work allows you to drop the height, and gives you a more comfortable seat as well. Zero negative aspects in the twisties either.