I have a 99FXST and I bought a cheap set of Aftermarket saddlebags with brackets for less than $100.00. I really only use them when we hit the road...two bolts hold the brackets (each side) and the saddlebags just rest over the fender (take off the seat toss em over and put it back on)
I also got a windsheild, but I find that the wind comes from lower down and comes upward, which drives me more crazy, so sometimes having one isn't/doesn't do what you think. guess it stops the bugs and rain from hitting you in the face. If ya want more comfort I know of folks who have deflectors for the lowers that stop most of the wind from swirling upward.
Other than that...all I could recommend doing without breaking the bank is rejetting carb/ K&N filter and pipes...this will give you several more HP over stock which you will appreciate. Also consider a new seat...the stock one is pretty comfortable but doesn't look the best. Also think of a backrest if you carry someone with you.
And finally, have a stash for beer money to enjoy yourself after a great day riding!
I'd be careful about throw over saddlebags. I have a friend who used them and the longer he kept them on the more the paint wore off the fender. I don't know if there is anything you could put between the fender and the saddlebags, so be cautious. Sask-man pretty much covered everything else. The way I interpret it, this is your first bike. If so, then CONGRADULATIONS!
Bubbas makes a really nice removable bag system but is expensive very expensive $180 not including the bags. The way I feel is I spent 17000.00 on motorcycle whats another 180.oo dollars you get what you pay for, my buddy bought some bags you throw over the fender he holds them to the blinker with a zipties and the first ride the rotor rubbed thru the bag and also thru his wifes leather jacket in the bag !!!!! LoL the jacket was 300 hundred hey I am already money ahead of him LOL
Yeah, gotta be carefull with the softy bags, your right they do rub. Mine rub against the swingarm and have wore off some paint and they have worn some paint under the seat. I never have a solo seat on so it's not too big a deal with me. You could put a rag under but all that does is trap dirt and dust and will act like fine sandpaper...so your stuck. You get what you pay for. My bags and brackets were cheap and I dont use them real often since I like the look of the bike without all the dressing. I have put inside the one bag a stiff peice of plastic and riveted it to the bag to stiffen it up and prevent it from rubbing further on the swingarm. You also HAVE to tie them to the tailights and to the bracket to keep them from doing what the guy above me said happened to him.
Look into Ghost Brackets- I don't have any experience with them but I was thinking about getting some. Around 180 bucks for the kit but you have to buy the bags and you don't need the U shaped bracket that goes on your fender because they have quick release and a backing plate that goes on the bags.