You have two primary components in any EFI system. The first is the manifold, injectors & air valves and the second is the actual EFI controller or what the OEM crowd calls the ECU.
In your situation the manifold and the air valves are by and large a single inseparable unit — although the Weber look-alike throttle bodies can be unbolted. That leaves the ECU and ECU choices to evaluate separately.
Before getting to individual ECUs, there are only three types of fueling models available. The first (literally) is what is called Alpha-N. The second is Speed Density and the third is Mass Air Flow or MAF.
The precision in matching fuel to engine fuel demand increases as you progress from Alpha-N to MAF based systems. That said, without a lot of specialized air ducting, a MAF based system is all but impossible to get to run with Weber look-a-like throttle bodies.
The Weber throttle bodies by and large will require a speed density style fueling model because it is so difficult to build the proper air ducting to make a MAF based system work properly. The use of a speed density based system instead of MAF based system only means you will need to adjust your fueling tables for changes in air density, like when you go to Denver or down to Death Valley. Those are extremes. You will need to tweak the tune well before you get to either of those extremes — but that is not a big deal but it is a necessary deal.
The next big event is going to be which ECU do you use. At the top of the hill you have names like Haltech and Motec. Those two companies will put your finished system (electronics only) somewhere in the $6K to $8K dollar window. Motec will get you closer to $10K for just the electronics.
In the middle ground you have some very good alternatives with names like FAST, Big Stuff 3, Holley etc. Most of these can be finished off for $3K to $5K but usually pretty close to $4K.
At the bottom of the pricing scale you find the factory manufactured MegaSquirt 3 Pro or MS3Pro as it is usually called, with an unheard of lifetime warranty! This system has been called the poor man's Motec.
The MS3Pro PnP comes in at $1,349, allows you to use factory Ford sensors and a factory Ford wiring harness if you want, includes a base tune (in speed density format) to initially get you up and running and provides sensor characterization tables to allow you to use any sensor you want w/o paying the exorbitant additional premium some providers add to an OEM sensor after repackaging should you choose not to use Ford sensors.
If you want to build your own harness they offer a top end version of the MS3Pro with much expanded I/O and a custom wiring harness (which you have to string and cut to length). The generic version is called MS3Pro Ultimate and is priced at $1,499 with the harness or MS3Pro EVO which is priced at $1,249 with the wiring harness.
The difference between the Ultimate packaging and the EVO packaging is just I/O channels. The Ultimate version is a full on, all things are possible, race inspired version. The EVO is for mere mortals who want to use a fully programmable EFI on their street rod. The beauty of the PnP version is the use of an OEM wiring harness and the availability of a base tune to get you going.
You will be impressed with how quickly the price of AN hose ends and AN hose adds up. Don't forget fuel pumps and fuel pressure regulators. It doesn't matter which system you choose there are some base line purchases all will require.
Although I did not specifically speak to it, all aftermarket systems include tuning software and data logging software. The MS3Pro guys also have a Bluetooth capability so you can program the ECU w/o the usual mess of cables and connectors - yet one more thing to consider.
Most all the systems are viewable at the website that uses the EFI name i.e.
Motec.com,
Haltech.com etc. The MS3Pro guys are here =>
DIYAutoTune