Re: Late model ford efi on a 390 FE
Last summer I dropped a 392 (SBF) into a 1996 mustang, and running a BBF off of a EEC-V based CPU (1996-2004) is definitely do-able. It's probably going to be more work and more money than you want, though. Here's the major issues:
1). You need a crank trigger wheel with crank position sensor (not a big deal, but it usually takes a little custom machining of the crank trigger wheel to get it onto your crankshaft pulley).
2). You need a camshaft position sensor. I made one by doctoring up a distributor. Ugly, but quick and effective. The only other way I know of is to custom machine the crank position sensor out of a late model ford explorer. There never was a CMP sensor for a BBF, so you'll probably have to go with the "doctor the distributor" route here.
3). You need an EFI intake manifold for 8 fuel injectors. Edelbrock, and few others make these for SBFs, but I don't think there are any for BBFs. You would need to take an existing manifold, and have it machined with bungs for fuel injectors. Probably a couple hundred for this.
4). You will need a very custom tune. This means that you will need to buy a handheld tuner, and learn a lot about the EEC-V (the route I went), or you will need to spend some quality time with a tuner and a dyno. This will be quite a few $$$ either way.
If you really want to go EFI, I'd avoid throttle body injection. In my opinion it doesn't really offer many advantages over a carb. It's a little more adaptable to widely varying weather temps/conditions, but I don't think it's worth the extra $$$.
If you have your heart set on EFI, I'd suggest trying to get a EEC-IV (1984-1995) based computer. The ECUs are pretty easy to find, and the programming tools are simpler and less expensive. You will still have the intake manifold issue to work out. The only reason I didn't go this route is that I had to have a OBD-II compliant EEC-V computer to pass emissions.