cfreidma, as far as your emissions test, make sure they did it properly. On mine, the guys couldn't find the obd ii port. Its to the left of the steering wheel. Also, you may need a new gas cap. That tends to be the part that fails the most on 450 emissions tests.
if the gas cap seal has gone (or is going) bad, that can also cause you to get a lower mpg as the gas can evaporate.
I agree with shifting it yourself instead or letting it shift automatically. I've found that around 3500 is the sweet spot for my car.
Also, make sure you have the proper oil for your region, that the air filter is clean, tires are properly inflated, etc. If you're running the A/C and doing a lot of hard accelerating up hills, that can cut gas mileage too.