What about a PTC (auto reset fuse).
Now that i think about it, If your poping 40A breakers you may have a fair bit more current than that flowing. You may want to spec a bigger PTC (or two in parallel).
You might need to do some testing.
Just be sure not to mount the PTC against plastic or it might cause melting.
I thought about re-wiring the entire setup using dual leads everywhere to reduce the strain on each individual wire and connector, thus going to multiple breakers was an idea. I could solder an additional female spade to the shifter buss where I needed an extra lead.
The battery harness on the toy side of the battery gets warm when in operation, not hot so it hasn't concerned me yet, possibly high resistance in the small connector tabs and changing out that connector is an option as well.
I wouldn't use a plain MOSFET, dual BTN7971B boards can be had pretty cheap and the ICs come with build in current sensing and drivers (current sense output is not generally broken out, but that can be bodged). More importantly, they are half bridges so you retain the braking capability of the standard controller.
Still need a PWM signal generator and some interfacing with the throttle pedal of course.
Would these boards handle up to 14V? I'm just basing that on a fully charged battery with some headroom.
That looks like something I would be willing to try.
ESC: http://tncscooters.com/index.php?route=product/product&path=41_73&product_id=159
Nice price, but it has undervoltage protection ... so not much good for you unless you can reconfigure the batteries to provide 48 Volt.
Since the motors aren't designed for 48V you're also looking at much higher peak currents and low duty cycles ... effectively it's only a 25 amp controller if you want to limit the voltage to 12 volt average to protect the motor.
The only off the shelf unit I can find which suits all your needs is this one :
http://www.motiondynamics.com.au/12v-48v-dc-pwm-with-current-limiting-single-direction-30a-or-50a-pcb-model.html
PS. yes these all work like ESCs, they use PWM to control the average voltage the motor sees and have a shunt to measure the average current for current limiting ... in theory you could build your own, but it seems a bit ambitious for a first electronics project.
I didn't notice the undervolt protection, was only browsing but obviously that changes things. Could this be bypassed?
The motiondynamics controller looks exactly like what I need, could I use a hall-effect pedal on this, or is it not needed? Darn thing is pricey though but it's worth a try or I could possibly get 10 other buyers to go in on it.
What would it cost to build one, from scratch is it worth building or are they cheaper to buy as is? This is something I feel comfortable attempting, could even get used to the Tek 465B I have sitting around

Filament bulbs can work as current limiters as they have low resistance when cold - e.g. a few 12v halogen bulbs in parallel, connected in series with the load might be worth a try.
This has been considered and is easily worth a try, just need to keep the heat down to a minimum and a fan-cooled box could be built.
Hack into the PWM circuit and have it automatically reduce the duty as the current rises.
Sounds fairly easy but this is where I'm poking around above my pay grade...lol However this is what I want to learn how to do.
I appreciate all the help, I trust we can get this to work, There is an upgraded 6-pin shifter module that eliminates the excessive switches and wiring and may be what I need to tackle this project with minimal clutter.