The over-temp will put the vehicle into a rich condition. The light may not be on, but a 1 timer (what a single event is called, it takes 2 events for the light to come on) may trip a rich running condition.
The computer will do that to attempt to cool the engine off by running it rich.
Clear the codes again with your reader. Even if you don't see anything there, most aftermarket readers can't read history, which is wear a 1 timer is stored.
After you clear the history, start the engine. Leave your reader plugged in, you'll need it again.
Now, with the engine warmed all the way up (temp in the middle of the gauge, not just getting heat out of the vents) and running, unplug the MAF sensor. The engine will probably die (sometimes it catches, but usually not). Now turn off the key, plug the MAF back in and restart the engine. Erase the codes again. There may not be a code in there, but again, just clear it anyway. This will clear any learned behavior stored and put everything back to square one.
The other thing that you mentioned was that you changed out a plugged fuel filter. The computer had to learn to deal with a lower fuel pressure (it has no way of knowing what the pressure is if everything isn't perfect). It did this by increasing the duty cycle of injectors, leaving them open a bit longer because the fuel wasn't pressured up to where it needed to be. So when you changed out the plugged filter, you had increased pressure at the injectors. The computer didn't know that you did this, so it's still thinking it's doing what it needs to do (by the self learn). So, you now have crappy fuel mileage.
Clearing the self learn should do wonders for your fuel mileage now.