My two cents:
First of all, stop worrying about what's "anti-GTD." Give the methods a whole-hearted try; if something doesn't work for you, try something else. (Or read the book again -- you'll probably stumble across something that will make a big difference.) It sounds like you've tried one thing; if it wasn't working, it's OK to try another.
Also, check out p. 38 - 39 (hardcover edition -- or Ch. 2 under Organize --> project support material) for some thoughts (brief, but helpful) about how to deal with Project support material and Reference files. (Or, to be really brief, you're OK.)