AEM CAI=If you're worried about water being sucked in, you only have to worry about that if your intake (filter) is submerged. It even says so on one of the stickers on your intake. However, as an extra precaution (I know Chicago, IL can get pretty wet sometimes), you may want to invest in a Bypass valve for like $39.99 (I think). Another alternative to your stock air box would be a SRI instead of a CAI. Downside? Greatly reduced HP gains from the CAI (still better than stock though). But if you're going to keep your CAI, replace the turn signal. You don't get that much better air flow like that. However, you could smash out your passenger side high-beam, and then run a (home-depot) self-made tubing straight to you intake.
If you really want to replace the CAI with your stock air box...remove the tubing from your intake (black plastic running from your intake, near your intake manifold). Put your car up on jack stands (you need to get under it). Take off the plastic lining underneath your fenderwall (so you can get access to the bottom of the intake). Remove. Easy as cake, right?
Wheel Alignment=No clue buddy...make sure your wheels are aligned (but you could check that by just driving straight without touching the steering wheel). Maybe tires under-inflated (check the same way). Weights on your wheels not balanced (check the same way). I got no idea why it does this to you only when you drop your clutch in.