Hi John,

Boy you are sure having some moments of contemplation with your engine.

If you engine has an EGR it does not have a vacuum booster of in the older retarded days of trying to make the engine run delayed or backwards to get cleaner emissions they used what was called a vacuum amplifier. It was basically a source vacuum pulling on a larger diaphragm to increase the amount of air displacement when it moved.

On this car there is no such thing unless you consider the very large brake booster behind the master cylinder.
What you are putting those two line onto is nothing more than a vacuum switch controlled by the ECU.
The ECU turns on the EGR during idle moments and it watches for a temperature change from a sensor in the EGR valve. If it does not see one in a certain time limit there should be a CELight to come on.
I bought a used car for a very respectable price because an independent mechanic kept charging the PO for other things so the PO got to where “shel would rather make car payments.

The switch will have one line to go to the top of the valve and is white in color. That line goes to the intake manifold over behind the throttle body via a rubber elbow.
The second line is yellow and goes on the bottom of the switch. It goes to the EGR vacuum diaphragm.
The switch only fails if it cannot vent that EGR line to atmosphere to resetting the EGR closed.
If the EGR stays open the engine will not idle correctly.
That could be a reason for your issue.
I don’t know what years the CEL’s started, so you may not get an indication of it’s operating or not.
My 1991 has it and cause that car to be up for sale in California.

Now as far as the distributor being 90 degrees out or on the wrong cylinder makes no difference in reality.
It just spins but where the wires are placed in the cap will make a difference.
Now with that said, the ECU might care as for the breathing sequence of cylinders that it is TUNED to and correctly adjust each mixtures to a protocol.

Oh boy in trouble now!
I’m thinking out side of the box here and the problem with that can be with how many corridors are outside.
Each corridor can have lots of doors to open. Every one should know where that can lead too.

I want to say that the timing belt would have a very hard time jumping off the intermediate sprocket.
I will say that the distributor can be indexed off one terminal location but moving the Number one wire to spot next door and then the sequence from there will make no difference as the distributor couldn’t care less?
That locating the number one as numbers on a clock is a state of mind only as long as you get the spark there. Who ever said 12 O’ clock has to be at the top or a watch can only be worn on the left arm.
Especially if there is no winding stem?

What may have happened is the flywheel got indexed off and so moving the wires accordingly got it have right? Easier than going under the car to rearrange the flywheel.

I still have no good answer for the engine running for “X” minutes and just turning off?
I already mentioned the ECUs programming. ???

Phil

Phil