I have installed this mod, but in doing so, I have removed the MK2 & MK3 Assembly Recepie for the factory buildings from "Factorissimo 3".
Is there a way to exclude these buildings?

I'm sorry but I'm not sure what you mean, could you clarify a bit? Vanilla Galore shouldn't remove any recipes.

I should have done my homework before confronting you. My bad (^_^")
Your mod is not the culprit. It is some other mod which removes he recipes.

But to clarify, I have this mod installed and know that you can craft it with an MK2 or MK3 AM. When I wanted to upgrade an MK1 to MK2, all items were spit out.

Don't worry about it, thanks for the bug-report nevertheless! (´∀`)b

(Bugs that are fixed before I even need to do anything are quite nice sometimes XD)