here is the thing,
I have both cars but I noticed some diferences on the engines. Basically on the turbo from w-126, it has a vacuum conection and the injection pump has a an aluminium device with electrical connections that it is different from w-116. Does it make a difference? Do I need to make a change or I would like to know if it's o.k. for me to put it the way it is.
Another difference that I notice is on the transmission presure control rod. Can I change the exahust manifull with the turbo from w-116 on my w-126 engine?
I would like to keep the injection pump from the w-126. If not possible can I just switch pumps from one engine to another?
Please advice.

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Just swap the whole engine and transmission from the W116 into the W126, and only swap the small things when they become an issue. I know someone who did the same swap back a few years ago and this is what they did.