SD=Speed Density.
If you're going to get another ECM, definately get one for a 5 speed, but don't forget to cut the wire to pin 30 (removing the pin/wire from the connector all together is preferable).
This whole situation just seems fishy. I can't put my finger on it, but it just doesn't make any sense. It "feels" more like an electrical problem, but I'm not aware of any that would cause your symptoms.
Tell you what, since you have a car you can borrow known good parts from, swap the distributor from your other '88, and see if that makes a difference. Moving the wires around on the cap, yet having the same plugs dead tells me the distributor is fine, but you might as well check it anyway, since you can, before spending the money on an ECM.
Ever think about buying a Harley?
Take care,
~Chris