Bruce Gordon and daVinci Designs both make cable splitters that work well. I have the Bruce Gordon's shift cable splitters on my S&S coupled bike and the shifting remains spot on after the splitters are disassembled and reassembled. daVinci also makes a rear brake cable splitter which I also have and it too works well.

I think the best way to do this would be to have two complete sets of bars, possibly each with a different stem. One bar/stem set would have the aero bars and bar-end shifters and what ever brake levers you use and the second set of bars/stem would have the STI's.

This is not unprecedented. Bruce Gordon make a bike called the "Rock and Road" which comes with a set of flat bars and shifters for off-road use and a set of drop bars for road use. His splitters allow a fairly quick interchange.