Otter, the short version is yes, by moving the white charge wire upstream to battery #3 my circuits stayed at 36v. The only other wires I moved were for my 12v tap, but that is a totally isolated circuit and does not play in this.
I assume you have an ITS. I would need to research your cart specs (year, system) to confirm.
The Alltrax will accomodate all 4 control wires, but the molded plug will need to be cut off of the E-Z-Go harness and be replaced with individual insulated spade connectors.
I purchased my controller secondhand so I had to visit their website and download some stuff. Hookup was easy, but take your time and don't guess. Doing it wrong gets very expensive.