I've never seen a CR 3.9 in pieces, yet, so I can't say with 100% certainty that the block is the same as anything else.
Going by the RGT 6.7s and 5.9s I have seen, the blocks are commonrail specific, in that the only timing case that works is commonrail, unless you drill some holes and move some dowel/locating pins around.
As far as a crankshaft goes, I overstated the importance of it, as it is possible that a 4b or 4bt crank will still fit in the commonrail block.
If it's the same as the difference between a 12/24 valve crank, the only difference in a commonrail crank in a 5.9 is the dowel that locates the tone ring on a commonrail.
Again, since I've yet to dissect a 3.9 CR (or it's 4.5 CR cousin), this is mostly just speculation, based on what I have personally seen while tearing various versions of Cummins engines down.
Mark.