Despite it all, I got done and after quadruple-checking the pins against the ATX standards I inserted it into my machine and fired her up.
I've redone some of my cable management when reinstalling the PSU. I ended up flipping the HDD upside down to make less of the power and SATA visible when the panel's off. I assume that this won't effect the drive's long-term health.
I really like how the ATX and EPS12V cables turned out. When installing the CPU duct I tore the plastic sleeving material where the EPS12V diverges from the ATX cable. I suppose it doesn't matter much because the damage is covered by the duct when in use.
With an eye towards cable management I'll show you the other side so you can learn from my successes and failures in this area.
This is the back of the HDD bay. Note the front audio cable stashed away as I'm not using it.
This is the back of the 5.25" tower. I've tried to run as many cables as possible through this area so as to keep them out of sight when in use. It's rather crowded now so if I don't have them properly arranged the side panel won't attach. That said, this plan is working just fine as the panel closes and the cables are hidden.
When the side panel, side exhaust fan, and CPU duct are back in place most of my hard work is rendered invisible but I can be confident that my airflow is just about as good as it's going to get.
Thanks for reading. Questions, comments, and criticism are encouraged.