Further update:
-pulled the idle air control valve and cleaned the intake screen which was caked with carbon
-reinstalled it
-started and allowed car to warm up
-it stayed at idle (a little rough)
-I checked the ignition timing. It was off a bit.
-Set timing to spec.
Result:
It's better than before. But, not perfect. It can still stall occasionally at idle. (starting when warm requires a tiny bit of gas peddle which it shouldn't)
The new engine runs very well other than now relatively minor the stall problem.

Things to do:
-install new air filter (done)
-replace fram PCV valve with OEM Honda one (need to order part)
-replace positive battery connection with OEM Honda one (need to order part)
-check and adjust valve clearances (done)
-retorque intake manifold in three equal steps radiating out from the lower-center bolt (done. Didn't use the 12mm crowfoot wrench.)
-replace a bunch of 3.5mm vacuum tubing (in transit now; doesn't look like I need to replace it, see next reply)

-if fixing any of the potential vacuum leaks doesn't fix the stall problem, I'm probably going to replace the mild-performance bistmoto cam with the one from my original D16A6.