If you can manage to modify an existing header and weld it backtogether i see no reason why it wouldn't work. If you keep the welds near the ends of the manifold you should be able to get a grinding bit in there and dremel away any "bumps" inside the manifold keeping it nice and smooth for the exhaust gasses to pass through easily. That is of course if you can find a header that would be suitable...

Good luck. If you can't find a way of modifying a header to fit i think your only choice will be to sell the engine and look for one with a regular port and exhaust configuration.