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This is likely an unnecessary question but I want to clarify. For the Enginseer, his abilities have the stipulation that "instead of shooting, choose X" or "instead of shooting, repair Y." My question is, may he do both in one turn?

I'd have to say "No". He only has one shooting attack to give up so he can't do both.

No they may only use one replacement ability per shooting phase that they are giving up. In the extremely unlikely event that a special rule gives them an extra shooting phase in the same turn, then and only then could both abilities be used.