The 400 does have a dry intake manifold, there is not a drop of coolant that flows between the heads, and the intake manifold, so do not worry about anything there.

why did you have the heads rebuilt?

is the coolant that is being burned off coolant that might have been in the exhaust from when the heads went bad before? Coolant that was in the cylinders from when you did the head swap? Pull your spark plugs to see any differences in coloration from one to the next..

How long have you had it running total since putting the heads back on?

Did it smoke right off the bat after firing it up? Was it running normally, then the coolant temp spiked, then it started burning coolant?

Did you use new head gaskets? torque the heads in 3 steps until you got to the full torque spec?

As far as putting heads on the "wrong" side... not gonna happen. Think about the spark plugs.. the pass. side is angling back, the driver side is angling forward. If you were to move the pass. side head to the driver side, the spark plugs would be facing forward, and vice versa.

IM not sure about the 400 heads in specific, but i know with some heads if the valve guides werent installed properly, or if the wrong size valves (stems) were used tons of coolant can pass them and enter the cylinder and burn off.

If its not left over coolant that is in the exhaust from when and if the heads went bad, or swapping the heads it may be a problem with either the valve guides, a cracked head...or a head gasket / warpage issue. Only other possibility i could think of would be cracked cylinder wall with coolant seeping from water jacket into the cylinder.