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Thanks, Windell!
My blog is here for anyone interested. Spoiler alert though, it contains code snippets. If you don't want to learn how I modified the Alpha Clock Five you should not click this link.
I found the problem! It was one of the solder joints on one of the resistor packs. I must have overlooked it because it was totally unsoldered. Just a bare pin sticking through the hole! Thanks for your help again!
Swapped out LED. It's not broken. Now I'm going back and double checking the soldering. It doesn't look like any of the transistors are backwards, and the resistor packs are in the proper configuration as well.
It turns out it was the FTDI Friend not being plugged in in the correct orientation... I was nervous to damage my hardware by forcing the leads... I jammed it on there and now I've got version 2.1 installed and running
Thanks so much, Windell.