Fuel filter would also be a good investment...
Also, how about unhooking the MAF or IAT or one of the other sensors to see if it will throw a CEL, just to make sure it works ?, then re-set it by disconnecting the batt.
Usually a CEL isn't "stop the car now SERIOUS" unless it's blinking.

Another option for the carpet & headliner is steam extraction. Though they should take it easy on the headliner.

My two cents 4 now...