To answer your question, yes. You can also connect the two B-junction boxes and run ONE wire (from either of the B-junction boxes) back to the 5-port (or 3 port for that matter).

yeah it works, as i've been running that sort of set-up the past two years. The beauty of e-Tube is that it allows for customization. I doubt you would even need a 5-port if you run that configuration. I currently have the extension shifters (and a climbing switch when needed) all connected to a front JC-41, and a wire from the front JC-41 to a 3-port EW-90. One port on the 3-port EW90 is plugged in, while the remaining port has a wire that connects to a second JC-41 (which connects to battery and derailleurs). In your situation, you could connect the wires from the two front JC-41 directly to the EW-90, and a wire connecting the EW-90 to the derailleurs, etc. Also, you could have things set-up so you have the following

Right bullhorn, Right extension, Left extension all routed to a first JC-41. Cable from left extension and cable from first JC-41 to a second JC-41; cable from second JC-41 routed to the EW-90.

Only caveat here is that if you are running an internal battery, the EW-90 has to be accessible.