I think you're on the right track with two-staging the fans. Couple things have already been mentioned (like alternator, and sufficient charging cable). I will also add a few:
I don't like the pulse width modified controllers. Yeah, they are cool, slow down the fan, but I want reliable. I would run each fan from that junction block, through it's own 30 or 40 amp breaker (whatever the fan requires) to a good relay (hella) and hardwire to the fan, the quick disconnects are notorious for poor connections. For the ground trigger side of the relay use a good quality temperature switch (I use BeCool) and tee in a manual override switch in cab in case temp switch fails or you just want fans on. Do the same for both fans for complete automatic or manual operation. All you need to change is the switch or the switch location (head vs. Intake) to affect temperature on/ off settings. If any of this doesnt make sense, or you need a diagram or part numbers, shoot me a pm, and I'll get it to you.