The Jeep is fixed. Believe it or not, it was the Park/Neutral switch.
I have to confess that I caved (again) and took it to a shop. A different one this time, and apparently an honest one. I'll be doing business with them in the future. I told them the whole story and what I had done to it so far. They checked/rechecked a bunch of things, kept a computer connected while test driving and had a fuel pressure gauge taped to the windshield just like I had done previously. After four hours of diagnosing they were still stumped. 6 hours and several test drives into it, the tech replaced the P/N switch, just to eliminate that code, and surprisingly the problem was gone.
That P1899 code has been thrown on this Jeep for years with no symptoms. I'd clear it, and in a few weeks it would come back. The internet said that this sensor told the computer that the car was in Park or Neutral so that cranking would be allowed. It always cranked fine, so I ignored it. Apparently the failure progressed recently, and this lagging/jerking problem emerged. The technician could see that the old sensor was consistently reading that it was in Park/Neutral while driving. Maybe it was previously just glitching occasionally, but recently became more constant.
So why would this cause the lag/jerk problem I've been having? The folks at the shop were not sure, and were surprised that it did, but theorized that the computer was doing some kind of partial rev-limiting/fuel cutoff action. Based on my symptoms, the computer must have ignored this input for the first few minutes, then started paying attention to it. I can't explain why the engine responded so inconsistently the way it did.
Thanks for all your help and guidance through this diagnosis. This was my first Jeep Forum thread, and a great experience.