Another good source for a carburetor upgrade is to get the Motorcraft/Autolite 2100 off of a 302 V8 car (that's what I did with the 2.8 I had in my Capri).
They're the same model number, and the same external dimensions, but the V8 versions will have larger venturis (meaning more air) and larger jets (allowing more fuel). You'll have to tune accordingly, but they are a bolt-on.
You sent me a PM asking how to dress it up to look good.
There are a LOT of dress-up parts out there for the 2.8, the problem is finding them.
http://jrcast.com/?page_id=79 This company in Ireland makes 2.8 valvecovers (valvecovers make the biggest or 2nd biggest impact in engine appearance). They're not cheap, but sometimes used sets show up on Ebay (as do other designs, there used to be several companies making them).
If you stay naturally aspirated, virtually any air cleaner with a 5 1/8" opening will fit on the 2100 carburetor, giving you a lot of choices. Valve covers and an air cleaner do the most for an engine's appearance (and a better air cleaner helps performance a little). If you go turbo, there are other ways to make it look nice (polished carburetor hat with silicone and polished tubing with stainless clamps).
If you want headers, you'll need to find a 1986 Ford Aerostar with a 2.8 in a junkyard... Or a used set of the old PaceSetter headers that have been out of production for years... both would be a challenge to find.
I'm on the other side of the discussion from
@jozsefsz though. I have a 1977 Ford Capri (imported from Germany) that had a 2.8 and a 4spd from the factory. While the 2.8 is a fine piece of engineering (and it really is, they're rev-happy, made great horsepower-per-cubic-inch for their day, and that snarl is fantastic). It's damned heavy for it's displacement (nearly as heavy as a 302 due to much thicker castings), is much harder to find parts for, and does suffer from a few design compromises that make getting more power out of them more difficult (the exhaust ports are the biggest obstacle). Those compromises can be overcome (
@jozsefsz is one of the guys that has done it), but I opted to swap a 302 and a 5spd into the Capri, and the 2.8 and 4spd just sit in the corner of my shed collecting dust, it was just much easier to get to where I wanted to be with that car than spending a lot of time scrounging up obscure bits and pieces (mostly from England, Ireland, and Germany, where these engines were used in much larger quantities and into the 80s).
Not telling you what to do. That's for you to decide. That's the best thing about a Mustang II. They're not worth a whole hell of a lot (though that's slowly changing, and already far less true than it used to be), so nothing you can do to one really affects the value, keeping you from getting boxed into keeping it "correct".