Does your mechanic still wear a mask? If not, ask why? An EGR is like wearing a mask, as you breathe in the carbon dioxide you just exhaled.

Ok, your "new" engine has the insulated bypass, your old engine has the EGR blank off plate, marry the two. There are several posts in this forum that detail the EGR delete process. To your point, rather than cutting off the smallish gray neck, remove the EGR and tubing, and fashion a sheet metal "bottlecap" and affix to the stub end using the same clamp that already exists in the system.

Reference the attached picture below, the red circle being where the bottlecap is applied and the yellow line indicating all of the stuff that can be removed to clean up the engine bay.

It's a tough one, I like D300's idea of stealth deletion. I've read of that once before, need to look into it. I agree that getting that crap out of the way has appeal, not sure how much it would be in my way however. I've never experienced an SDL with EGR in place so I'll check it out. Not sure what the chances for coming into grief with smog official type people is either but would be nice to avoid.

Disabling vacuum to the EGR valve has the same effect as installing a blanking plug and blanking plate on the EGR ports. You just don't have to do anything any more complicated than blocking or removing the vacuum line. There is a very strong spring inside the valve that keeps it pushed closed when vacuum is removed. Done and dusted. No parts or tools required. It's your car, your time, your money.

Diseasel300 is 100% correct, you can easily disable and leave everything in place, the default position for the EGR is closed with no vac signal. You are also in CA, so you need to determine whether or not you are subject to any emissions testing/inspection. I would think that you would be except from an age perspective, but maybe not.

You also have more room under hood in the w126 than I do in the w124. In my case, ditching the EGR made room for an EGT sensor and an Oil Catch can and was well worth the effort, but again, I'm not subject to any inspections and have owned the car for nearly 20 years and plan on owning it 20 more, so as mentioned, your time, money and risk/reward profile should drive your choice.

When you mentioned a BB before, do you use the right size to plug the vacuum line so that it doesn't even look at first glance to be disabled? I mean plug it then reattach it.

But to the question of not knowing where to put the three different colored wires in the jack, was all much ado about nothing. As the donor car was not going to be used again, he just cut most all of the wires. I mentioned it to him today, he agreed it could be a small difficulty - we went to look at the 'new' motor and there was the jack, still attached to the IP, with about 8 inches of wire sticking out. Not sure if he will just use crimp connections to hook the wires to those on the car. The method I would think better would be to use the old method of wrapping two wires with a bit of wire strap, about a quarter wide, crimping it in place then soldering, followed by sliding the preplaced shrink fitting over the joint and heating it. That way you could solder them in-line and then use the shrink insuator.