Adam,
I am happy for you in terms of getting it up and running again your battle is only half over, though. The Ron Francis kit is an excellent kit and does a stunning job of cleaning up the wiring in the car. Entry-level kits are about $300 give or take and vehicle specific kits are $500 or a whisker more. I am not sure what the replacement ECU cost but let's say it was around $300. That puts you halfway to the aftermarket system price-wise, but with all the limitations and undocumented programming vagaries of the OEM ECU.
From an emissions and vehicle registration perspective, the Ron Francis kit will either have difficulty passing the referee's visual inspection or will fail the inspection in the more demanding testing some states do. If you manage to pass the visual inspection (I don't think you will) when they hook up or try to hook up the emissions computer to your OBD II port (if it's still there) the whole show will come to an abrupt halt.
If you are going to roll the dice from an emissions inspection perspective the aftermarket plug-and-play alternatives give you a much better starting point and at least a recognizable OEM OBD II port for the inspection station. In states like California, you simply are dead meat — it has to be 100% OEM or have a CARB certification like Whipple and KB do, otherwise from an emissions certification and vehicle registration perspective, you're on the outside looking in again,
The worst part is when you are all done you are still saddled with all the original engine speed limitations caused by the slow OEM ECU not to mention all the undocumented (by Ford) programming methodology for the ECU.