After a conversation with the EI Commander company, I realized I had left out a couple of things in the Pmag wiring. The ground to the EI Commander is tied to both Pmags and each Pmag gets grounded to the case. Ran a wire from Left to Right Pmag to link the grounds to the EI Commander and Ran the Pmag grounds up to the top of the case where the baffle support mounts. Seems redundant to me, but thats what they want.
