I've been using Litestep for a few years now, I've done a lot of tinkering in that time and I want to start getting into module programming. I've got a good grasp of C++ and Java but haven't touched the Windows API yet, so I'm at a loss when it comes to interacting with Windows behind the scenes.

I'm not looking for someone to teach me everything they know, just some tips on what to learn about, books to read, that sort of thing.

no books needed. look into simple modules' source codes, see what API methods they're using, look them up at MSDN.
as long as you're simply doing some basic module programming, that'll suffice.