I had alot of similar problems as you.. I have almost completely flat feet...next to no arch whatsoever, and when I put my weight down on my feet, the probably widen by about 30%...i imagine this is from years and years of wearing skate shoes, sanuks and flip flops. I had Burton Ozone's, Salomon Factions, Vans Revere and all of them hurt..I tried 4 different brands of insoles ranging in price from 20-80$ and they did very little to help. In fact, they tended to cause MORE pain because of my low arches.
I kept hearing great things about Rome boots and went and tried on a pair of Libertines. I found that they had a consistent width throughout, and TONS of padding and cushion inside. My back foot cramps up occasionally on my first run of the day with them , but other than that, they are the most comfortable boots I've ever put on. I have also decided to steer clear of Boa and Speed Zone lacing type systems..with regular laces, I simply CAN'T overtighten the outside of the boot, yet i can still control where i tighten certain areas. I would really recommend giving them a try if you havent already. They changed everything for me and have really made my riding much more pleasant.
Never Summer Evo 153/Restricted ReFlex Cartel
Gnu Danny Kass 156 BTX