I went through a maddening process trying to cure the shudder on my '96 and finally gave up after 4 different sets of injectors, 2 injection pumps, 2 valve jobs, and tweaking with the gov. springs. The thing that helped most in the end was the DDP Stage II injectors but it still has a slight miss.
There are 2 things I suspect to be the cause. . . #1) pulsations by the lift pump could be causing some hydraulic harmonics inside the pump (fuel hysteresis) that leaves one cylinder lacking for fuel at the right RPM. Change the RPM a bit or give it a little more throttle and the condition subsides (engine smooths out). So I wonder if regulating the fuel and evening out the LP pulses would help the problem.
#2) or it could be governor related where at the right RPM the springs "bounce" a little and the governor drops fuel for a few microseconds (the bottom of the spring bounce) in time with one particular cylinder (causing it to seem like a slight miss). I think the problem with the P7100 governor is the springs are too "springy" and bounce too much. . . if these springs had some damping, ie. a "shock absorber" of sorts, I think pump hypersensitivity, shudder, the herky-jerkies, etc. could be improved considerably.
Vaughn