Keith,
I am currently building one. My thought was to at least build one according to the classical methods before I started with the mods--although I was very tempted to follow Ty's approach. My gear is done, and I'm happy with it. Ready to start installing ribs when I get some time. Didn't have any problems so far. I was actually more worried about the extra hassle of covering and finishing with the gear in place. Ty didn't mention it, but that is a really big advantage of his method in my opinion.
I used hobby shop J-bolts, but put them in a wire bender and bent them a full 180 degrees. Then I trimmed them so they wouldn't bottom out on the spar web. The way it finally went together, I was able to keep the threaded portion of the bolt in tension, and avoid bending loads.
Don't worry too much about putting bolt holes for the gear thru the spar. All of the flight the bending loads in the spar are at the top and bottom surfaces and the center pretty much only carries shear. Same with wing torsional loads. It's the covering that has to carry the most load, not the spar web. The bigger issue is avoiding excessive landing loads on the spar. Land smooth.
I can't post pictures here, but if you want I can send via iphone. PM me your number if you think it would help you.
Good luck with your project!
Dave