What I did to mine:
Cut off all of the connectors
I took it all apart
found the +12V cables and the black ones picked maybe 5 of them and wrapped them around my banana plug on my charger
heatshrink
neatly cut all of the other cables
take the green cable out of the main mobo connector and connect it to one of the black ones.
That acts as the on/off switch, but it also has one on the back.
The wire that is uses for the computer plugs aren't very good and you really need to make sure you attach a lot of them to the banana plugs. I would say 10.
If you want to be able to unplug the charger, just buy some female banana plugs and install them in the side of the case.
Do a Google search for something like "convert computer power supply RC" and you'll find a few nice guides.
Your charger will pull 360 watts right? That means that you want at least 30 amps on the 12v rail. Even then yo may have the voltage drop too much, I would look for one rated for 33-35 amps just to be safe. It also depends on if you are planning on charging both batteries at 180 amps.
Thanks for the clarification on the multiple rails, I thought it might work, but I guess not.
If you don't mind the color, this one looks nice
http://www.newegg.com/Product/Produc...82E16817148005
Or this one for $40 with free shipping
http://www.newegg.com/Product/Produc...82E16817713004