You'd be severely limited trying to tune the Dual plug ECU. No one has disassembled the code yet so there's really no way to get in there and tweak tables and such. There's a fairly good sized group of people who run the stock Dual Plug DIS setup with a turbocharger. They keep the boost down around 6-8psi so the stock ECU doesn't wig out and fuel and air can be manipulated by means other than reprogramming the ECU.
By going back one step in evolution to the 4-plug distributor fired setup, you open the door to easy tuning, and an ECU that you can reprogram even if you can't set the clock on a microwave.
