Kevin:
For the time being, it is best to set your mill to Furl at 60 amps if it is possible.
If you are going to connect two controllers to attain 100 + amps, I would suggest that you do a offset setting.
Set the bulk charging of the early dropping controller to drop about 0.1 volts lower than the second, this way no hunting will occur and both will operate smoothly.
You will need a good ballast controller that indeed should be a PWM controller even though one of the messages by "electronbaby" says something against it -- to control resistive loads which is the natural way to dump the excess energy from the mill ( of course one can direct such power to heaters, for water or what ever ).
You indeed have a basic problem --- 12 volts --- with high power, 100 amps is to much to work with with low volts.
Even 24 volts is too low voltage but the current can be handled a bit easier -- preferable 48 volts -- that starts to "give" problems around 3 KW.
The relay driver may OK for a load that is energized few time a day, for power sources that may be energized many times a day, like 100 to 1000 times/day, I would not suggest such arrangement -- the relay will last few months, high current relays may have 50 to 100,000 cycles, this is a short time indeed.
With a PLC - Programmable Logic controller with the addition of several MosFets one can have a 100 + amps charger controller and as well the ballast controller all in one package.
The PLC project may require additional items, like current detector, voltage detector and the capability of having the charge controller with MPPT capabilities to harvest additional power from the mill.
Also, with the PLC, one has a PWM controller to attain better charging capabilities with true MPPT profile.
This PLC needs to have high frequency PWM capabilities -- they are available.
Learning to program it is a process that may take time for some.
Nando