I am by no means an expert, but from what I understand the larger exhaust is likely hurting your MPG, however it's probably not a huge amount. The lightweight rims are always a bonus. I wouldn't worry about taking in intake air from the engine bay, as GRU said, having a simple warm air intake should be working in your favor.
How is everything else mechanically? Brakes dragging, running rough, etc?
Do you have basically the same driving that you did with your EX? Simply a different route or type of driving can have a pretty serious effect on your fuel economy.
Since your car is a 2000, I would recommend getting an UltraGauge or Scangauge II. If you search the forums here they have been discussed a lot, and everyone I know who has gotten one has seen instant improvements in fuel efficiency.
