It's most likely the tranny. I believe it's slipping (3rd gear is a problem). When the hesitation occurs, is it while the car is shifting into/out of 3rd?
I'm not an expert, but I do work on cars. From what I know and have encountered, hesitation problems are the result of dirty fuel injection systems, old/faulty distributor (don't know about how that happened), and faulty transmissions. It could also be the O2 sensor from what I'm told, but seeing as how you had fueld/air induction service, I doubt it's any of the above.
By the way, please don't use below 91 octane fuel (or below whatever your manufacturer recommends)
This could damage the engine.