ikin, I would restore the car back to stock as much as you can, like putting the stock airbox in with new filter, not your old one. I would also put the stock exhaust back on. I have a new 02 GTS with 40k miles and I barely passed smog in cali. I just moved to La from Vegas so I had to get smogged for initial registration. I barely passed because I left my custom free flowing exhaust on cause I was too lazy to bolt my stock on, and also I didn't hook up all my vacuum lines because I forgot how they hook up. ok, technically I should not have passed the visual, but I just bolted the sensors on to my stock airbox somewhat behind it, so it looks right. I had to put the stock airbox in to pass the visual inspection, because I had a non-carb custom Intake
made(my secret weapon).
Also, I would run a high quality fuel system cleaner like red line's to clear out your system. You might want to invest a $100 OBD II scanner so you don't have to keep on running to autozone, etc to borrow a scanner as you fix your car. I bought the Innova Obd II for $130 with a $30 rebate. It works great.
Also learn about trip drive cycles and about all the monitors on your car and the procedures you have to follow to have the monitors complete their diagnostic. In CA, you need at least 5 monitors to have run successfully and come back with no DTCs (Diagnostic Trouble Codes) to pass one part of the functional smog test.