Ok, had time to look at the truck again:
Fuel filters are pretty darn clean -- coarse was perfect, some buildup on the fine filter.
Put the pump back in, started the engine up (after building pressure), and our testing methodology was correct. The pressure readings follow fuel pressure down (verified by pulling fuse for pump, dropped pretty quickly to 30psi or so and kept barely idling).
Still annoyed at cold start (will test again tomorrow... read on), but it runs pretty well heated up and in closed-loop still, and the long-term fuel trims appear to be pegged at +25%.
We're going to double-check resistances from the ECU end of the harness on the injectors (thinking maybe harness?), but we're pretty much at a loss. Anyone got any ideas?