Would smaller throttle bodies 36mm or 38mm with the large port head help at all?

Correct. Porsche gave the early 3.0L engine way more port than they required (39mm) for the cam and intention of the car. They also did it with the 3.2 Carrera (41mm). These were not ideal ports and they were utilized on production vehicles.
Port volume has a far less effect than cam choice, but it does have a tangible influence. An example would be that 3.0 liter small ports have a peppier low/mid rpm than the Carrera 3.2. I also prefer the midrange of a 2.7RS over a 3.0L with identical specs. But all the example I have given are drivable builds that do everything they were supposed to do nicely.

JMZ's potential build is supposed to be a back up race engine and now I'm not confident what direction he his headed. Figure out what you want out of the build and do your best.

Ideally we match a port size to a displacement, cam and the intended RPM redline.

Compression is dictated by cam choice or visa versa....but ideally by cam choice.

So if you go down in cam, you will need to go down in compression.

Smaller volume in the intake and exhaust will pull a big cam down the rpm range some.

I have seen ex race motors brought back to the street just with smaller intake and exhaust and they seem to run just fine.

It certainly helps, but its all about port velocities with the camshaft's lift thats critical. This is measured with pitot tubes on the flow bench as you know. :)