I've owned this vehicle since new. Well, my dad had it and then I got it. He never touched anything.
I'm sure the box is the spark controller now. It's interesting, the box itself is small, but is contained in a plastic holder that makes it the size of a TBI ECM. This is then strapped into the vehicle. It's like they planned ahead on the form factor of the ECM, or the California vehicles needed the bigger computer for the CCC and then they kept the form factor into the TBI years.
Anyway, it's the spark computer. A little thing. I'm pretty sure the other box must be the cruise control.
I think I must have pulled the wiring out of that box when I did my TBI swap and just completely blanked my memory on it. I'm using the big grommet to get the TBI stuff through.