Every time I've had that problem, its been a door lock or fuel door lock or trunk lock. Occasionally I have knocked something loose, but you've checked for that.
Normally it seems really wierd at first like there are 100 different options all converging. But usually it traces back to either the green or red line on one of the vacuum actuators. What I mean by that is that the actuator itself is bad in either the open or close port. Therefore, you simply begin by plugging one door at a time. Note: I usually suspect one of the back doors or the passenger front. Its relatively easy to plug those doors with golf tees.
Once you find it, it seems so easy.
Hey, at least its not electrical....
Don
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