2. Unless you want a cover that might do more harm than good, $100 to protect a $35k car is a darn good price. It's probably less than your deductible
You should look up the pricing on a California Car Cover.
3. I don't recall seeing any factory mud flap options for the car, so they aren't totally off base by saying they don't offer any. Look into a set of Rally Armor or DRT flaps.
4. That's the WRX tire size (TireRack booboo). The factory STI size is 245/40/18 with 18 x 8.5" wheels. Not all wheels will clear your Brembos (spoke clearance) - be careful. There are lists in other areas on NASIOC that list Brembo-compatible wheels. If you do go with 17's, you'll want a bigger tire than 235/45/17's. Probably 245/45/17's (much closer rollout to the factory size).
Enjoy your new car!