So I've been poking around with this board and I'm pretty sure I've narrowed the problem down to one of the two dual-package 60V MOSFET ICs on the Inverter Board/Riser Card (which can be see as the "wall" on the right half of the power board separating the inverters from the transformer.)
The story:
I began a systematic effort to try and test all resistors, diodes, semiconductors, and capacitors on the board. Obviously, testing some components while on the board can be tricky, but many of them can remain on the board and give a reasonable indication of proper function. What I noticed was that on one half of the board I could not use my multimeter's diode tester to induce a charge in the capacitors; I was continually getting shorts across all of them (even the ones I had replaced). Through strategic desoldering of one or two components, I was able to isolate the short and discover it existed on the inverter board/riser card. One of the power pins on this card was shorted to the ground pins. I desoldered the inverter board/card from the power board, and all shorts on the power board disappeared.
Closer inspection of the inverter card/board revealed that one of the ICs on the board, a 9945N 60V N-Channel MOSFET package, had its source, gate and drains all shorted together. I managed to desolder this IC and probe it off-board to confirm it is indeed the source of the short and not the board.
During this whole process, I was also able to confirm that the transformer does put out the required 18V to the inverters and the 5V to the logic board, and that as suggested earlier by budm, an over-voltage condition likely existed that prevented the transformer from performing properly.
So I'm in a position to obtain a new 9945N from Mouser and solder it to the inverter board/card. Though before I do, can anyone offer their insight on how/why one of these ICs would blow? I was told they sometimes just die. But if that's not the case, I'd hate to solder a surface-mount component just to have it die again from whatever killed the original one. Anything I should look for on the inverter board/card or power board to see if something damaged the original IC?
Thanks for the help!

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