I think the underdrive pulleys are beneficial so it would be better to keep the pulleys and get a higher flow water pump. In the mean time, going back to the stock pulley may work.
A MAF computer is not programmed for any specific injectors which is what makes them so great for building up the engine. The computer will add or remove fuel depending on the feedback provided by the oxygen sensors. As long as you have a properly calibrated MAF sensor to match your injectors, you should be fine.
One question about this, though. I remember you mentioning that you aren't using the stock ignition system or stock distributor. How does the computer know what RPMs your engine is running at if you don't have a TFI module and the distributor to go with it? If it doesn't know your engine RPMs, how can it look up values for proper air/fuel control? The look up tables are based on load and RPMs. Also, wouldn't the computer just stay in open loop mode if it doesn't detect a TFI module?
I don't think a little oil in the intake will hurt you much. Do you notice blue smoke or anything when you step on it? I'd inspect a spark plug every now and then and make sure that they aren't getting fouled.
I'm going to look into the drilled hole issue a little more.
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351W 89 Mustang GT Convertible