Configuration space integrals have in recent years been used for studying the cohomology of spaces of (string) knots and links in $mathbb{R}^n$ for $n>3$ since they provide a map from a certain differential algebra of diagrams to the deRham complex of differential forms on the spaces of knots and links. We refine this construction so that it now applies to the space of homotopy string links -- the space of smooth maps of some number of copies of $mathbb{R}$ in $mathbb{R}^n$ with fixed behavior outside a compact set and such that the images of the copies of $R$ are disjoint -- even for $n=3$. We further study the case $n=3$ in degree zero and show that our integrals represent a universal finite type invariant of the space of classical homotopy string links. As a consequence, we obtain configuration space integral expressions for Milnor invariants of string links.