If you thought that buying a set of castings for an engine would simplify your life by now you've learned that castings can be a real bear to hold - especially so when you're trying to machine orthogonal features.
I solved some of these problems by building a tooling block that is, in effect a strap-on set of reference surfaces for small castings.
The block is sized to fit into my milling vise in all three orientations. It has T-slots sized to fit a range of miniature clamps I made. Most importantly, two adjacent faces have provision for removable fences. In place, they really help in getting things lined up and constrained while the clamps are set. Once the clamps are set they can be removed so milling operations can "go off the end" without chewing up a fence.
A non-obvious advantage of this system is that mounting and aligning the workpiece can be done sitting at the comfort of the workbench after which the whole affair can be dropped into the milling vise.