If the engine has been swapped out:
* It is very possible/likely they used one or more incorrect rods.

A couple of pictures would help diagnosis.
* Linkage neutral/at rest wide pictures.
* Maximum accelerator (forced to floor) linkage pictures.
* Try to get pictures of the injection pump stop in Neutral/at rest and Maximum accelerator positions.

As a note, you may need to alter/fabricate one or more thrust rod.
I suggest if you MUST:
* Cut the existing rod in the middle, to weld or silver solder additional pipe/rod in.


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