No...fuel filter is whatever.

Don't get sucked into the "high-flow" fuel filter business. I can't remember if your car has the in tank filter or not either...

Google the seafoam stuff...do it before you do the tune-up...1/3 in the gas tank, 1/3 in the oil, the remainder in the brake booster...and you'll have to have someone rev the car so it doesn't die from the massive vac leak.

Pretty sure the psi @ the rail needs to hold at least 44~...and not bleed off. If it does you've got a pump issue.

I'd clean your Throttle body for one...that's a huge issue with the drive by wire cars. Then...plugs/wires/clean the coils/ICM...then I'd get rid of the cat...or replace it with a high flow one...or just buy a 3" bolt-in downpipe from ZZP if it hasn't been addressed yet...they can clog. It's common. Another thing I would do is check for vacuum leaks with carb cleaner while the car is running...do LIM gaskets...etc...if it has never been done...and for the cone...yes...rip out the box and just leave the PCM there...it won't go anywhere...and bolt the 9" cone to your MAF. Done and done.

Anything else?