The first thing I would do is look and see if it has the dual radiator hose intake hoses from the TB, if it does, split it at the first set of clamps and see if it has the trumpets in place, many of them had a set of noise tubes that barely were bigger than your thumb in ID. Hack the ends off with a hacksaw and put the hoses back on
As far as the engine, I run that ECM with a 489 inch Mustang, you can go as mild or wild as you want, but we have had some success just going for additional torque in the past with a 331.
Massachusetts used CA emissions limits and we had to meet them, using a 331, zero deck and a smog legal cam on a 91 back in the early 90s, we just did a plug and play with the short block and gained noticeable torque. Like anything else, the details of the build make the power. The injectors do have a little buffer, especially if you add an aftermarket regulator to increase pressure, but you can't go wild.
If you wanted to play, I would do a zero deck 331 or 347, probably 347, smog legal headers and adjustable fuel pressure regulator, pick a smog legal cam to match the RPM range you want to run and compression to match cam and fuel. With heads, an intake and tuning, it would be a monster, but the tuning usually consists of an aggressive recurve which often can turn the emissions tests upside down
If you weren't as gutsy, I would do a good quality rebuild, .030 over with a modern ring pack, zero deck build 5.0 with as much compression as I could to match the cam specs, and then a good valve job with some bowl work and smog legal headers and a good exhaust.