Idle slow to return to normal
Idle returning slowly can be affected by many things, depending if it happens in gear or park/neutral. I would try the throttle follower table first. Try increasing the decay rate, so it goes away faster. Most people adjust tables by 5 or 10% at a time and then go drive.
For stumble upon acceleration, I would say that the main VE table needs adjusting via the RAFIG procedure(sticky at the top, also in EFIlive help section).
There are many experienced members/tuners(wait4Me, Jimmyblue, Old Geezer off the top of my head) on this site who share their expertise. If any of them have something to say, I would take it as gold. good luck.
That's a start in the diagnosis. That filter is not where it should be.
A. directly in the fan wash. Try a search. That set up is in question in many t/s theads.
B. The MAF is sandwiched, and should have strait tubing before and after.
C. The intake alone is a reason to do a tune.
Post the tune file and a data log.

