I had random (very infrequent) same type problems in my 93 400e. and the check engine light is on all the time too. I reseated the fuses in the base module, and I loosened and sprayed (pbblaster) the electrical grounds. The check engine light went out and it hasn't stumbled since. However the CE light has decided to let me know that it is still there, so I might try the procedure again, maybe clean other grounds.

These cars are very sensitive to electrical issues. (I had a 400e that started coughing whenever the after market radio was turned on.)

But I think you need to concetrate on what happens after the car warms up. since that's when the problems shows up. you can fool the car into thinking it's not up to temperature to determine if it's electronic or vacuum related.
I would think that if the car thinks it's still warming up, it should run fine would indicate electrical issue, while if it still stumbles when it thinks it still warming up would be vacuum/egr/other emissions.

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