Nice info about the Cyclone, I'd love to build a 69 fastback with AWD.
To the thread, the AWD supposedly can handle about 500HP, for how long, that's a good question. I'm headed that way with a KB blower on my 302.
Unless you are staying stock and married to the old Mustang operating system, don't use it. Sell it, and get the vastly far superior Explorer OBDII PCM and system. The OBDII can be tuned to handle any and all modifications. The EECIV has driveability issues with all highly modified engines, it should not even be considered.
You will need the whole front dress to match the PCM, the timing cover, balancer, water pump, distributor drive pickup, wiring harness, etc. Don't start with a 99-01 for your 98 model. You have a returnless fuel system, and need the matching 95-98 PCM. I'd get a 98, to work with your PATS. Buying a whole donor vehicle or drivetrain would be the cheapest and easiest route. Good luck,