Mumford,
I had something similar not too long ago, and it just happened to be about a month after my lift pump had failed and had been replaced. Naturally I assumed that my VP was going south. I made an appointment at the dealer to get the documentation process going (still under warranty) so that my complaint was at least registered, even if they were unable to duplicate the problem.
Mine would act up like that for several blocks, missing, running rough, no power, lots of blue smoke, especially after sitting for about 6 hours or more. Sometimes it would start to do it out of the clear blue, even with the engine up to temp. Every time it would do it, I would make a mental note, then write it down once I was stopped and it was safe to do so.
I changed the fuel filter, drained the separator, disconnected my high idler, all the usual stuff in an attempt to rule out any other possible causes, and I met no success.
The solution was actually very simple. I started checking where I had bought fuel for the last few weeks. Lo and behold, I had purchased fuel each time at the same place for 3 weeks, except once, where I tossed about 15 gallons in at another station. During that period, it ran better, but would still go into limp mode from time to time.
I was fairly low on fuel at this point, so I stopped to fill the tank, but I stopped at a different station. Viola! Ran like a charm. Since that time I have fueled everywhere but the station where I purchased the bad fuel, and the problem has not occurred since! Oo. Naturally, I canceled my dealer appointment.
I don't know for sure if your problem is from fuel or not, but I would certainly give it a try. The place where I got the bad fuel is a truck stop - they sell LOTS of the stuff, so I did not expect any problems from the fuel. A friend of mine with a 12 valve gets fuel there all the time and he hasn't had a problem.

. My fuel pressure has been right up there where it belongs the whole time too.
The next step I need to take is to go back to that truck stop and put some fuel in from there and see if the problem comes back. If it does, I'll go to the OTHER truck stop across the highway, even though it's harder to get in and out of, and won't go back to the bad one again.
Good luck!