according to the internet, the 2.8, 2.9, and 4.0 are all considered part of the same V-6 family, known as the Cologne V-6. But while being part of the same family, many of the parts are not interchangeable.
The 2.8 uses a gear drive timing system (camshaft turns opposite direction of crank) while the 2.9 uses a chain drive timing system (camshaft turns same direction as crank).
Exhaust valves are located differently on the 2.9 also.
Im guessing (GUESSING!) that you would need to swap the heads and intake from the 2.8 onto the 2.9 block in order to run the 2.8 carb. (Or Holley 2150 2 barrel if I remember right, is the choice replacement for that pile of crap electronic carb it came stock with). But with the exhaust valves being in a different location, Im not sure that the pushrods would line up with the older heads.
Most guys actually convert the 2.8 over to fuel injection using the throttle body injection off a rear wheel drive 3.8 v-6 ford from the 90s (t-bird, crown vic, NOT taurus).