Don't worry about the air filter.

If you're having tranny work done, swap the shifter back.
If you're having anything drivetrain related, (that doesn't require them taking off the shifter boot, put the stock handle back on. The big chunck o rubber in the handle will make even a quality aftermarket shifter feel nearly as crappy as the stock shifter.

(Personally, I don't think the stock shifter is all that bad with a different handle as long as long as you don't beat on it too hard. If you're gonna beat on it, then the stops in aftermarket shifters are a must. But, if you're just looking for feel, it's a nice compromise that's not gonna hurt your warranty.)