Why not stick with 500 amp peak per board and then stack another board for double the capacity?
Spreading the load is sometimes the best solution when you reach the brick wall of available circuitry / limitations.
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I have been watching this discussion of heatsinks with great interest because I work with the hardware in servers on a daily basis. A good 80Mx40M 12VDC cooling can can dispel over 450 watts of thermal energy on an Intel Server. Why not do the same with your controller?
In fact, here is a cooling fan with a built in temperature probe. You can put the probe in the metal fins and move the fan to the end of the board. As the temperature increases the air flow will also increase over all the heatsinks.
Antec 92mm Smartcool Case Fan-Best Computer Online Store Houston Buy Discount Prices Texas-Directron.com
MPaulHolmes, PM if you want some.