Hi
I will limit my comments the MS MPPT 60
Why did you go MPPT? Vs PWM with panels in parallel?
That controller works great with 60voc input power - allows smaller easier to manage and lower cost wires from the array to the controller
What VOC do the panels produce?
Suggest you go a bit larger say 70 amp output fuse (and use a switchable breaker)
On good solar days you should easily see high 50amps from the PV array
(My little 550watt array easily produces 40+ amps and as you with only two 6Vdc GC batteries which work just fine for us)
I used switchable breakers for the array and load connections from / to the controller - makes it far easier to isolate the controller (it draws current from the battery when in long term storage, makes software upgrades easier, etc..
Suggest you hook up the voltage sense line and the Temp probe from the controller to the battery.
Plus the Ethernet and the serial data cable - you will need to setup the operational parameters via a computer
Strongly suggest you do not simply use the dip switches and set / forget the install
Any plans for the remote meter?