I've been using Orbitools for a few years now and while expensive, they work in cross-drilled holes better than I would have EVER believed possible. Getting all the parameters in your machine is the tricky part, or course, but once dialed-in, they work wonders. We had a part where 4 holes intersected, we ran the orbitool in there and in the end every one of the complex surfaces had a perfect and smooth radius.
http://www.jwdone.com/orbitool.html