SM-EW90-B 5-Port Cockpit Junction Box connects Di2 shifters to the frame junction box via SD50 E-tube wires. The 3-port Cockpit junction box does not allow for the multiple satellite shifting options like the 5-port but it is a little lighter and sleeker.
All Di2 components on the bicycle require the same firmware version. Using Di2 components with different firmware versions may cause malfunctions. Use Di2 system checker to update component firmware from http://e-tubeproject.shimano.com/