WHOA, crazy Marco!
Refresh my memory, you're not running a fuel pressure gauge correct?
I'd suggest fitting even a mechanical one so it can be watched on the dyno.
Given the fact that once the air temp sensor had a brain fart (and read -25) your AFR's under boost went back to normal, I would almost lean away from a pump/filter/injector issue a bit given that ONLY the change in air temp readings restored the proper fuel amount. If the filter were plugged up really well it probably wouldn't have been able to return given the fact that its clogged.
Is it also possible that during the first lean AFR situation that the air temp might have gone buggy? Did you notice it at the time?
Check out all the wiring and the sensor itself and go from there
EDIT: To me though, the most suspect part of the fuel system would be those 1300's as several people have had issues with them, but also, I don't know the age of your pump and filter. If anything, a fresh filter won't hurt...