I had the same issue, and it had multiple causes. If it stutters when right at increasing rpm (accelerating, even light), you could have a sticking fuel pressure regulator. Since you have replaced that, I posted that symptom for the next guy that reads this. it took me a very long time to find the cause, since ti was so ephemeral.
Ultimately, I found that the rear injector had a bad crimp in the connnector that attached to it. I had done wiggle tests, to no avail. The way I found it was I disconnected the injector wires from the injectors. Then i connected a meter to the contacts for a single injector (out and return), and connected a jumper across where the injector connects at the other end. I set the meter to audibly indicate continuity and really got with the flexing fo the wires, starting at the injector connector. Then I actually found that the bad crimp in the rear injector. The problem was that you had to move the wires "just so" or there was continuity, explaining why wiggle testing revealed nothing.
The symptoms were like yours: warm up period was OK, then subtle, random, and rare stutters, mostly at a rolling low rpm. Apparently, the warm-up delay was due to the softening wire insulation as it warmed up, allowing for additional flexing to the "just so" position. The low rpm aspect of it was likely due to the additional shaking of the engine at the lower rpms, under load.
If you are going to jumper and probe at connectors, make sure you do not damage contacts by inappropriate probe and jumpeer ends. The contacts in the ECM connector are particularly susceptible to internal damage (also causing intermittent connection problems).
Enjoy,
Rich P
