Ford F-150 (2004-2008) :: Idle Rumble Came Back Slightly And CEL Came On

I bought a '05 F-150 with a 5.4 with 112k miles on it a few months ago. It had been sold from an auction, looked really clean, and a good price. Not long afterward it started having issues with running rough at idle. That's when I found this forum and began reading. Tried different things but it only got worse and finally had a shop look at it. Cam phasers were not doing well. Not a cheap fix but more involved engine work than I had ever done so I had them do the work.

It ran fine for a few days and then the idle rumble came back slightly and the check engine light (CEL) came on. I read the code and it came back with a number that indicated air flow was an issue. Internet search said to clean the throttle body. Some threads on this site also said do the Mass Air Flow (MAF) sensor while I was at it. Much has changed since I used to work on cars as a kid. Everything has it own cleaner. I cleaned the MAF sensor with MAF cleaner. Cleaned the throttle body with throttle body cleaner (it was beyond filthy) and a toothbrush. Put it all back together (started late and it was dark by now) and took it for a quick run to see how it had improved. Instead of smooth, it started running even rougher, and within 100 yards went into fail safe mode. Now my mood is getting darker. Park it and go inside to watch the Aggies in their bowl game.

Good game but the truck is still running rough and I am losing confidence in my ability to do simpler things on it. I get up the next day and run codes on it. It had three codes all pertaining to air flow or the throttle position. I am thinking I screwed up the throttle setting somehow when cleaning or maybe only put the MAF sensor in upside down (that seemed unlikely since the screws only seemed to line up in one orientation). So I open the hood to check the MAF sensor just in case and find to my embarrassment that, in the dark, I failed to plug the MAF sensor back in. The problem was a loose screw holding the tools. I plug the sensor cable onto the sensor and take it for a ride. It runs great. Life is good. MPG is climbing higher on the onboard display. My confidence is returning even after humbling mistakes. After everything, I still love this truck.

So, now for the tune-up advice. The truck runs well but still rumbles slightly. Based upon everything, I believe it was well cleaned before it sold but maybe not fully serviced. Spark plugs were possibly never done. I intend to do a tune-up on it but do not know what has already been done so I'll assume almost nothing. The air filter looks brand new. The serpentine belt has nicks so that will be on the list. I am thinking of changing the following:

Spark plugs
Spark plug boots
fuel filter
serpentine belt
PCV valve
Oil was changed when the cam phaser work was done. So the advice really boils down to a question:

Is there anything else I should consider changing or doing or cleaning? I have not worked on cars much in the last 30 years but am beginning to enjoy it again.