Hello Mark,
which objects do you want to photograph? Is there so little space between your objects that your lytro lightfield camera with 112 mm length won't fit?
In opposite to your lytro camera image stacks from my Canon A590IS need to be aligned because of the little sideways lens moving when I photograph image stacks with CHDK. This is an advantage of your lytro, the images should be match perfectly. Is there no output of a sharp photo from near to far in the lytro software?
1 cm macro distance with your old Ricoh CX1 is quit good, but if it is not always working
. If I were you, I would look for a comparable Canon CHDK camera and shoot with a small tripod my image stacks.
In my first answer I forgot to mention Photoacute which has a very good image alignment, noise reduction, depth of field extension and superresolution image improving.
In Helicon Focus software there is also a option for 3D object generation from image stacks, don't know how accurate that is. But because this is a standard technique in microscopy there should be other solution for this for example in ImageJ (which is free).
As you also mentioned microscopy, an old stereo photo technique in microscopy is to tilt the probe.
I hope it helps a little bit.
Karsten