Basically the 2 systems you have are identical so use the best of both.
But like1BadAction said neither will run the E trans... you can still use everything and re-pin the newer ...7427 PCM and add some wiring for the trans.
What's involved with a Banks power system?
In the end you'll need a cable to hook up to laptop and get some data logs for getting the most out of the tune that comes on the chip inside the ECM/PCM but a stock one will run it.
Also spend some time seeing what other guys are doing to supply fuel to the TBI unit. It will probably need 2 pumps... one to supply fuel that far and one to keep the pressure suffeicent... and a return line.
Nice Ride!
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