You really need to get that 180 degree thermostat to continue further Mods. It will help with knock. You will never get an answer from Overkill on the PCM. I used a ZZP tune and hand no problems with them in my 04 gt and Comp g. I changed to an Overkill and it was better than ZZP setup wise. I have all of 04 Unlocked on my HPT if you want to work something out. Otherwise if I were you I would get an HP Tuner. You can do a lot with it and be able to get your car tuned properly. which in turn will give more power, better acceleration and shifts. As well as disable codes so it will pass inspection.
Front plog would be ok but probably not needed unless you plan to mod further. You need to careful with a stock transmission as you mod.
I would do-
HP tuner or custom tune
180* thermostat
2.5 Downpipe.
NGK TR55IX plugs- you can stick with the 104s if you wanted
high flow air filter
3.6 MPS if you really want to drop pulleys. Must be tuned well.
Fuel pump rewire.
Plog if cash flow permits.
Having these things will allow you to mod in the future and have the tuning ability to do it properly.