Tom, the pricing I quoted is right from MM's site. The OP mentions nothing about replacing the shaft, stuffing box shaft log, repainting the engine bay etc. if so, I could see the cost reflected in more parts and more , a lot more labour.
But let's not overestimate the complexity of an atomic 4.
It's a whole lot simpler than this:
an engine which can be torn down and rebuilt in less than 10 hours. fewer bearings, simpler valve train, half as many heads, no separate cylinders or a split case to align and torque down, etc.