That was what I was going to do before I did the swap on my 99. I did everything except for actually putting it back together.
My plan was to use the explorer electronics, and whittle the EFI system down to work as standalone. Not that difficult, I just never got to the point of testing it. Never paid to much attention to the air box, was probably going come filter.
Having said all that, I probably wouldn't go that route in your position. The big plus to going with explorer is that it controls the 4R70W and the parts are included with purchase of a donor. You've got the swap completed and don't need an engine donor, and you're using a manual transmission.
I don't know what engine you used as the basis of your swap, but if it wasn't the Explorer you've got a lot of things to change to make that system work. For starters you need the Explorer crank pulley, which is made for a 50oz balanced engine, so if yours is 28oz it is strike one. You'll need the Explorer timing cover to mount the crank sensor, along with the rest of the accessory drive to make it all work together. Essentially, if you don't have an explorer engine already, you're doing the swap again.
In your position I'd look to doing a Mustang AL9 based EFI conversion, or going with one of the assorted aftermarket EFI systems.