Wheels

Again my father gave me his 1989 carbon fiber trek. He gave it to me with some ****ty wheels on it just to get started with. These wheels were 7 gears. I later bent the rear wheel, so he gave me the wheels he bought for the bike that he raced with. The new wheels are 9 gears. Obviously when I put the new wheels on it shifted funny, and quite frankly sucked. So when I took the bike in to have them set it up for the new wheels, the guy at the bike store said I would have to guy new shifters. I was under the impression that you can tune bikes to the wheel/gear sets. Is this true, I just find it weird because my dad use to race with the 9 gear and i know he didnt change the shifters.

How many speed are the shifters you currently have?
Perhaps the bike shop guy thought your shifters were screwed.

Concerning Shimano gears, most modern rear hubs will fit 8, 9 or 10-speed cassettes.
You could probably even space one out to fit a 7-speed cassette, if you really had to.