Your combo sounds pretty nice...do you have the Performer or Performer RPM heads? I'm assuming you got the 1.9 intake valve heads. Please tell me they're not the 2.02's.  So this hesitation is the motor...NOT a delay in kickdown from the transmission or something right?
All I can chime in and say is..when I first got my car, it had a really bad hesitation. It made zip for power below 3000. It'd boil the tires to oblivion, mostly because they were bald, but it was seriously lacking go until 3000-3500, where it literally threw you straight back into the seat. The problem was I had several broken fuel injectors that were leaking fuel....so I had several cylinders with not only irregular spray patterns which was throwing the efficiency and burn out of whack, but the ends around the pintles were broken so they were constantly leaking fuel out, causing me to flood in lower rpms.
Just figured I'd mention that...hey...you never know. I'm actually really curious to see how this works out cause my new motor is getting a Cobra intake, Performer RPM heads, and an E-303 cam running with a stock MAF and stock 19 lb/hr injectors...I was told by several people that the 19's were enough, and others told me they'd be concerned about leaning out. I'm really curious to see how your car runs now since we'll be modded so similarly.
Good luck bro. 
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'91 Mustang GT 5.0 AOD Daily Driver
Current stats: NEW 302 short block, E-303 cam (@.050, 220/220, .498/.498, 110 degrees), 1.6 roller rockers, Performer RPM heads (aluminum, 1.9/1.6, 60cc chambers), Cobra intake, Granatelli 75mm MAF, Billet AFPR, Equal-Length Shorty Headers, Off-Road X Pipe, Flowmasters, 4.10 POSI
13.73 at 103.8, ~2.2 60'
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