Heh...I have a 1-1/2 size difference in my feet. Sucks when it comes time to buy cycling shoes. One is always a little tight and the other one always has a wrinkle in the toe from pulling the straps tighter than they were designed to be cinched.
Lots of guys swear by shoes that have been fitted with or come with heat molded foot bed insoles. I've never tried them, but I can see them providing a more even support, maybe a little better overall fit and I'm sure they do correct for some foot deformities/atypical foot geometry, etc. You can buy the moldable insoles separately or buy a brand of shoe that comes with them. There are LBS/dealer fitted versions and do-it-yourself versions...pop it in a toaster oven or some such thing.
Cycling shoes, like saddles, are VERY much a piece of equipment subject to personal comfort and idiosyncratic preferences. You sound like you are a pretty experienced cyclist. I'm sure you know pretty much exactly what works for you if you put in 6K+ miles in a year. I'm also sure you've been in on those conversations where two guys are raving about how nice their Sidi Genius 5 shoes are while the two guys next to them cringe and state they couldn't donate their Sidi's to Goodwill fast enough.
The old saying, "If the shoe fits, wear it!" is probably never more appropriate than when considering a cycling shoe. It's GOT to be comfortable first and foremost. If your local shop sells Carnac's, Lake's, Pearl Izumi and Bont's...try those on and pick a winner. And once you are positive (after a few hundred miles of riding in them) your feet love those new shoes, buy another pair or two before the manufacturer drops them from the line.
Just like you can't pick a saddle out from a bunch of pictures, I'm not a fan of buying shoes thru the mail. There's no replacement for having a half-dozen boxes of shoes on the floor of the local bike shop and swapping back and forth and back and forth...you may drive the staff nuts for an hour, but your feet will be comfy and pounding out mega-Watts for many, many hours in them.
One thing that always drove me to distraction was the quest to find a shoe that fits, is comfortable, has a retention system that doesn't bind and adjusts perfectly to my instep, looks decent AND has the 'just right' heel lift that works with my calf muscles and pedaling style. Too flat of a sole...cramps. Even going by the 'look' of the sole, it wasn't until the cleats were dialed in an a couple long rides were done that those new shoes were put back in their box or donated to a youngster on the junior team. Sometimes even Cinderella and Prince Charming have an easier time getting it right.
