I think a chip is supposed to control more than just timing...I'm pretty sure it also controls air/fuel ratio so your 5.0 won't run too lean or too rich. I think it has a different map to help the stock computer better utilize your modified setup. I'm also talking about a custom chip based on your particular setup. I'll try to find out more than that for you.
Let me know if your car runs any better... 
BTW...I too am a seriously detail oriented anal retentive bastard....and this whole thing is making me absolutely nuts.
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Midnight Blue 89 GT... 306... ported and polished aluminum GT40's, MAC Long tubes, MAC power pipe, Flowmaster 2 1/2 cat back, GT40 intake with ported upper and lower, B-Cam, 24lb injectors, 77mm Mass Air, 65mm TB. World Class T5, 3.73's, Centerforce Dual Friction, FRP aluminum radiator, Victor Jr water pump, Pro 5.0 shifter, Crane adjustable FPR, 255lph fuel pump
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