I'll begin with the question, which is intrinsically interesting:
Let M be a manifold with some submanifold Y. Suppose that $W \rightarrow M$ is a smooth, proper map. Does there exist another map $W \rightarrow M$ homotopic to the original that is ALSO proper and transverse to the submanifold Y?
Let me note that I am definitely not assuming the manifolds are compact. John Francis sent me a nice proof in the affirmative if I'm willing to assume that everything in sight is an open submanifold of a compact one, so for all practical purposes I have what I need. However, I'd still like to know if this result is true more generally, and I can find nothing in the literature.
Why I care: This question came up while thinking about the geometric description of complex cobordism given by Quillen in "Elementary proofs of some results of cobordism theory using Steenrod operations." I have a geometric description of the coboundary map in the Mayer-Vietoris sequence but as of now it relies on the answer to the above question being "yes."