+1 on what Dan and Tony said.
Everyone has a favorite EFI system, eventually you will too. Right now (even though yours is fixable) your #1 job is to select the replacement EFI system you want to use going forward.
While there are lots of systems out there I have a personal preference for the DIY Autotune MS3Pro systems in large part because of their performance, feature set, price and widespread understandable Youtube help vids. Here is the link =>
MS3Pro Ultimate. There are excellent systems available from any number of providers. The next best bang for the buck systems are the MS3Pro and Holley EFI products.
You can go from the bottom which is somewhere around the FAST system you now have to the top which is a Motec. I believe you will really want to be somewhere in the MS3Pro / Holley EFI play pen. MS3Pro will mean about $2K or less when you're done. Holley will mean about $3.5K when you are done and Motec is, well stunning pricewise. They usually ask you if you own your own home before the sales process begins and when you see the $10K+ price you understand why.
I know this is not what you want to hear but it is real. You can suture up that antique system Roush delivered to you and it will always be problematic or you can replace it with a more modern implementation that works as expected. Bitter medicine, I know but as real as it gets.
BTW FAST has some, more modern (and higher priced) systems available. You should also look at them and firms like Haltech which has some very credible offerings although again at higher prices
I believe in the end you will likely gravitate back to the MS3Pro. If you do be sure to check out the MS3Pro Plug and Play offerings. They will allow you to use an OEM Ford wiring harness out of a salvage yard or ?. The big deal about the OEM harnesses is they are mass produced, factory tested (although yours will be used) very durable and for the most part done. By, 'for the most part done, I mean you might need to lengthen or shorten one or more sensor wires but the PITA job of creating a harness from scratch has already been done for you. The MS3Pro PnP will plug right into the OEM wire harness ECU receptacle — which is also nice.