OK, I figured out what my voodoo needed to be...
Even after reverting to my pre-Caldigit hardware config, I still could not get the thing to fire up with the boot volume in the PCIe slots, no matter which one, got the folder with the ? mark after a long grey screen time. This lead me to go back and do what I did when I first got the 840 / Vx2 card. At first I put the 840 in the PCIe card slot, cloned the original boot volume that was in the lower optical bay. Once it was cloned, I swapped drive positions and rebooted from the new drive in the optical bay to establish it as the primary boot volume. Then I shut down and simply swapped drive positions, 840 in the PCIe slot.
I simply had to redo the position maneuver to re-establish the 840 as the boot volume, only this time I did it with the 120SSD in the PCIe card in slot 2, 840 in the lower optical bay like the day I first got the drive. Presto, booted fine.
So I repaired permissions and powered down then swapped the drives, 840 now in PCIe slot 2 and the 120SSD back in the lower optical bay. Once again, boom, fired up without incident. Now, to be fair, I left every peripheral unplugged except for my ACD 30" and it's USB keyboard plug. Once I deemed everything was working well, I started plugging things back in, FW800, eSATA, USB3.
So far so good, happy little family of drives and such. I tend not to reboot very often so I am going to run with it and see what happens.