Hmm... I forgot what car you have, forgive me, but if its boosted then definitly clean the MAP sensor. Also, the throttle body...
Fuel filter can be another option, but a complete fuel system clean would be a good idea. I wouldn't go to the shop though if I were you, especially for that price. Buy some Sea Foam (just the name, not actually foam from the sea lol) and that'll clean EVERYTHING out. Injectors, fuel lines, etc. You will have to change your oil after this though, but I've seen amazing results using this stuff.
As for not being able to connect... Thats pretty strange. Unplug your battery AT the autozone parking lot for 5 mins. Plug back in, and immediately read your ECU. If that doesnt work I dunno what else to tell ya.
Hope this helps a bit