Random thoughts, I’ve been playing with FE’s since the 60’s, I have 3 right now, 2 are in cars making in excess of 500 hp each.
I think it’s great that your son is interested!!
If the trans modulator was bad, it could have been sucking tranny fluid into the intake manifold, causing the smoking. I know you replaced it, but leave it disconnected at the intake and plug the vacuum connection while troubleshooting the engine and trans separately.
Stuck oil rings have already been mentioned. They might loosen up with time, or not, if they are really gunked up.
When the engine is idling, after up to normal operating temps, pull the oil filler cap and check for blow by. That will tell you a lot about the condition of the compression rings.
Valve stem seals may be cracked and rotten, they can be replaced without removing the heads, it is a slow and time consuming process, but it can be done. If the valve stem guides are bad, you’ll have to pull the heads.
The FE’s in pickup trucks were lower compression than the FE’s in cars of that era, due to piston deck height. Parts are still available, they just cost more and you may have to wait for your local parts store to get them. Performance parts for FE’s are probably more available now than they were when I was racing them in the 60’s, but they are pricey. Look to Summit or Jeg’s for stock or performance parts. Most guys at O’Reilly’s, Auto Zone, etc won’t know very much about FE’s except what the computer tells them, unless you find an old guy or a FE fan. Just Google “Ford FE” for lots of internet FE forums.
Best wishes with your project! Good times for you and your son working together!