Blue,
I have almost the exact setup on my 88 GT, except 73mm MAF., equal shorties, TFS heads, and a Mallory ignition.
I have the EXACT same problem now. If I gun it, at 3500 ish I get a terrible stutter and then it catches and goes on. It is very disconcerting. My 306 is only 3000 miles old. I have checked/swapped plugs three times, checked distributor, new coil, wires, checked TPS, IAC, new 255lph fuel pump , filter, Billet FPR @43 PSI, new O2's, temp sensor,etc, etc.
I do know that my TB (65mm BBK) plate is sticking. At least around idle, and I am thinking of upgrading to a 70mm with a new TPS and a Pro-M 77mm MAF. I ahve also been chasing the "wandering idle" problem too, especially at warmup. After the TB upgrade, I guess it's time to voltage check injectors and the computer.
By the way, my 88 doesn't have a check engine light. So it's even more fun.

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1988 GT Convertible
331 10:1 TW heads, GT-40 intake, MSD, TRW flattops, B Cam w/ 1.7's, MAC exhaust, 24's, 70 TB, 76 MAF, 3.73's, Pro 5.0, Koni's, Anderson PMS, Wideband 02, yatta, yatta...
One week with new motor, two speeding tickets...joy