Been doing this for my last few projects and loving it. Using yeoman helps simplify the process a ton.
Now if there was only a simple way to exclude all of the styles that are never used across a site I'd be able to cut my CSS down like 75%, but that would probably take a headless browser crawling the whole thing.
As another commenter pointed out, you can recompile the .less files, excluding what you don't need. You can also use the web customizer in our hosted docs at getbootstrap.com.
I'd recommend using the bootstrap source at first, and pulling out the modules you don't need from the bootstrap.less file. Because they are separated semantically, you can probably guess which pieces you won't need, and then band-aid from there.
Now if there was only a simple way to exclude all of the styles that are never used across a site I'd be able to cut my CSS down like 75%, but that would probably take a headless browser crawling the whole thing.