Tech By Trade:
Thank you for the suggestions. It already had a new fuel filter less than 500 miles ago. The injectors were replaced with the reman engine, and not certain, but I believe cylinders 2 & 6 are on opposite fuel rails.
Also, there was no 'feeling' of a misfire. Just a sudden, smooth large reduction in power and RPM, then resumption to normal in a half mile or so. Still ran smoothly, even when the power was reduced.
All:
We went looking for something else. The shop that replaced the engine did a very poor job of reinstalling the wiring surrounding that engine, so we approached this as if it was an intermittent failure in the wiring. With a little detective work and wire wiggling, several problems were found. At one point during the troubleshooting, the engine wouldn't even start due to the input voltage to the new ignition module being missing. (That shows up on an OBD scan.) Wiggling the loom would make it start, then die.
My (new) mechanic found several places in the loom where the insulation was either missing, compromised, or there were suspect connections. A couple of sessions with some new wire, a solder gun and some shrink sleeve seems to have solved the problem. Got about 200 miles on it now with no problems
I'll let all know if this holds up.