Here is my detailed Di2 installation with parts list, if it will help.https://forum.slowtwitch.com/...ost=6572184#p6572184

My post above will probably answer most of your questions directly... That said:

You can use any of the bar-end shifters (SW-R671, SW-R9160, or SW-9071). You just nee to decide if you want 2-button or single-button.
Ditto the brake levers-- you can use any of the current or prior-gen Ultegra or Dura Ace brake levers with single or dual shift buttons.
Your junction boxes depend on your wiring-- how many wires you need to join and where. In my case, I used the 2-port Junction A with a 4-port Junction B in the cockpit and a 4-port Junction B at the bottom bracket. Most folks use a 5-port Junction A and a 4-port Junction B.