Do the slices from the two experiments overlap? Or is there a gap between them? Or do they neatly interleave, like a perfectly shuffled deck of cards?

If you want to start from the raw image files, then you can use program to3d to assemble the volumes. The only tricky part is making sure the filenames appear on the command line in the correct spatial order.

If you want to start from two volumetric datasets assembled from each of the two scans, then probably the simplest thing would be to write a little script to use 3dZcutup to cut each volumetric dataset into 20 1-slice datasets, then use 3dZcat to assemble the 40 1-slice datasets back together, and then delete the temporary 1-slice dataset files.