There are many aftermarket standalone systems that are SD, as well as Mass Air. They both have pros and cons.
Regarding using the Ford Factory EEC's, I ran a V1, a SD cam. Edelbrock heads all on a SD EEC with a Johnson Motorsports chip- I am sure you can get a tune still burned for an SD EEC if you want. Untill you start running large duration cams or huge amounts of boost, I say you can run a SD EEC. The issue is the stock SD EEC is pre programmed with set AF tables and is not as adaptable as Mass Air. With Mass Air, once you start adding an HCI and/or a power Adder, you will need to match the Mass Air Meter to the injectors as well as getting a tune on the Mass Air EEC. If you make mild changes, the Mass Air EEC will be able to compensate better. In stock form, the SD car is actually faster as it had a more aggressive timing curve if I recall correctly. Ford went to Mass Air for emissions mostly as well as better driveability
Most people will convert to Mass Air as a precursor to making further mods