The 50MM Throttle Body does work with the 2007 110 inch arrangement. In fact the SE throttle body is pretty much 'plug and play', everthing is idenitical to the stock 48. Even the TPS voltage was dead nuts on. Also, the flanges that come with the 50 MM throttle body are correct for the 110 inch heads. Dont let anyone try to tell you to waste your money on the Kuryakin adapter flanges,, YOU DONT NEED THEM, and they wont work.
You are going to see a major improvement with the 50 MM swap. I use the DTT ignition and revied one of my recent data runs. Fuel starvation begins at 4800 rpm with the stock throttle body. You can blame the new injectors on this one and a simple injector swap would do a lot of improvment too, But the 110 inch has lots of room for deep breaths and the larger TB will really help that out.
Make sure you share your performance story when your done.