I had a ton-o-trouble doing this. In the end I made a guide-pin out of an AN bolt and that did the trick. In short, I took an AN3 bolt and put it in the chuck of my drill press (a poor man's lathe). Then I held a file against the end of the bolt to taper the end. Then I rounded the tip with a wheel.
I put the gear mount in place with one bolt (a little loose), then in another spot used the homemade guide pin to align the rest of the holes. I put a bunch more bolts in place. Finally, I removed the guide pin and put in its place an unmodified bolt.
I'm not at the end of section 29 yet, but when I get there I'll be using this method again to permanently install the gear mounts.
Here's a link to my build log.
http://airplane.athomeinthewilburness.com/2013/12/08/fwd-ribs-bulkheads-bottom-skins/