You have 2 choices for reading temp to control the fan. Engine coolant temp and Radiator temp.
Personally, I like to read the outgoing radiator temp since its the Fan's job to keep the coolant coming out of the radiator cool and the job of the thermostat to keep the motor up to temp.
Some people like to read the temp of the coolant coming out of (or at) the motor. As I see it, when you do that your trying to control the engine temp with the Fan and so is the thermostat. Also, it puts you behind the curve since you don't want the fan(s) to be running all the time you need the setting high enough that it doesn't run while your on the freeway.
As for wire, just make sure it is as least as big as the factory wire was. I'm running 8 gauge on the Mark VIII fan on the Van and on my friends f-150. We are both running breakers. I run a single 100 amp manual reset and he is running a dual 50 amp (in parallel with bus bar) self resetting. We tried lower amperage breakers with with the Southern Az heat and under hood temps we were popping the breakers even though the running load was < 40 amps. I may try switching to a fuse since its less susceptible to heat.
If I understand what your planning on doing, your going to have a bunch of room in front of the radiator and want to put a big single trans cooler there. For big coolers, I like the MaxCool coolers from TruCool. I am personally running the model 47391 on the Van as the only trans cooler. Its rated at 40,000 GVW rating, 45,000 BTU. The Van with Trailer and X behind it is 14,000 (I think thats right). The highest I've seen the pan temp get is 160F and that was going up hill near the AZ/CA border by Yuma in mid 90's temp.
I got them from here and they have all kinds of sizes...
http://www.bulkpart.com/Merchant2/merchant.mvc?Store_Code=2&Screen=CTGY&Category_Code=tru-cool-hd
I don't know if the two 1000 cfm fans is going to be enough to keep things cool, especially off-road. In the hotter climates, even the black magic fan wasn't keeping 1st gens cool.
Hopefully that info helps..
~Mark