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Check to make sure that you have coil power on the run circuit (key on, no start). I ran into the same type of problem going from 1st Gen to 2nd Gen electronics. There was a difference in those as well. The first gen (79 RX7) ignition had power to the start, but no power thereafter and another wire carried power during both start and key on. The 2nd Gen (87 RX7) had power on one wire except during start and another wire that had both. If you have the coils hooked to the wrong wire, it could cause this problem. Best bet is to break out the multimeter and see which wires have power when.
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