I've been fighting with my vacuum system for quite a long time and have done extensive research however I'm a bit stumped at this point.

Here's the issue, with the door lock check valve connected to the system the locks do NOT function and the car does NOT shut down. Easy fix right? There's a leak in the door lock system... Well maybe not... I've used my Mityvac to pull a vacuum on that check valve with the car off and all it takes is a few pumps and the doors lock/unlock as they should and HOLD vacuum for several minutes (I know it should be days, I'll deal with that later). So we've now determined that the yellow check valve and all door lock valves and connections are good, right?

So now I check the amount of vacuum at the booster line (all other connections blocked off for testing) and I'm getting a rock solid 21 Hg, so now I tee in the shut off feed line I can still hold 21 Hg, the tee is proven good... I then remove the shut off line then connect the same tee to door lock check valve assuming after several minutes of evacuating the resevoir I should be able to hold close to 21 Hg as well and operate the locks (same as I did with the Mityvac). I cannot generate more than 4-5 Hg after 10 minutes of idling. And with that low of vacuum the locks will not function and the car will not shut off (if the shut off is connected of course). WTF?

Please tell me where my logic is failing me, thanks!

your logic is fine.
most likely, when everything is connected, tension is placed on a connection somewhere, and it leaks... enjoy the chase!

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You might try plugging one end of the vac supply line (the solid yellow one) to the master door lock switch in the driver's door. Then use the mity vac to pull vac on the line to make sure it's holding vac. You could have a cracked line, or there is another check valve under the dash that could have gone bad.

You might also try plugging the end of the reservior line and pulling vac to make sure that line is not leaking.

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I've done all of that, the entire system holds vacuum when applied with the Mityvac. Only the car vacuum pump can only sustain 4-5 Hg.

Did you try using you mity vac to pull vac directly to the vac reservoir. I know it will takes a lot of pumping, but maybe the reservoir is leaking. I guess an easier way to test that would be to pull the connector off the res. and plug it. Then tee in your mity vac into the door lock system like you had before and start the car and see what it read. If it's still 4-5" then the leak is somewhere else. If it goes up to 21" then it's the reservoir.

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Good call, I'll give that a shot. When I sealed the resevoir connection with clear RTV I did hook that up separately and was able to pull 20ish within about a minute on the .6 orifice (not the white one) connection however the .5 (white based) took quite a long time to build anything up... So I am reading these vacuum diagrams correctly, the door locks/climate control/shut off should be fed by the .5 orifice and the transmission/egr via the .6 orifice?

Not sure what car you have. But if you have a W126, have you checked the condition of the vacuum pump diaphram and or rubber lines inside the trunk mounted pump? I have found a few where the vac line had become detached. And one that needed a new diaphram.

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Woops! I have an 82 300D W123. I'm not aware of a truck mounted vacuum pump, is that a W126 thing only? I have gone through my entire lock system, pulled every door panel and checked every line. They all held up to 20" of vacuum and the door locks operated as they should when manually pumped. So my only thought is that there may be a small enough leak that cannot be overcome by the fairly weak vacuum pull of the stock pump but can easily be worked with the hand pump or my vacuum pump is failing...