In my experience, I believe I only ran across a couple of significant differences between a 39 and a 46 216. I wasn't aware that a water pump was one of them.
I spent last winter putting a 1939 216 in my 46 truck.
If memory serves me correctly... Different crank, flywheel, and flywheel mounting flange, (4 bolts vs. 6 bolts with keepers, if I remember correctly). I believe there are some differences in the rear seals. There is also a different oil distributor location.
Ran into problems with that last one, when I had my manifold split according to measurements I took off of the 46, rather than the 39 block.
I'm going to have to look at the water pump I pulled off of the 46, when I get home this evening. I had saved it, so I'd have a spare if I ever needed it.
