I have an 04 also.
1) Those bolts on the side hold those chrome side panels on the bike. Gotta have them, but I'd order some stock ones from Kaw. Swing by a dealer, they may have some in stock, and if not, they can order them. They should not be very expensive. Make sure you have/get the big chrome washer thingy (and the rubber gormet, and the steel backing).
2) Because the 04's have the bug head light (called a "nacelle") it takes a special faring/wind shield.
3) Yea, I'd say whomever had it before you was probably not 6'4. That windshield is probably funneling the wind straight up your nose
4) Pulling the gas tank is actually very very easy. There are several threads here talking about, just do a search.