I'm a bit nervous to write this in case I somehow Jinx it, but it appears as though the charging system is fixed. On your advice I tried too track down areas where I would be losing V's and decided to re strip, clean and make better connections for everything that I changed. looking at what I pulled apart, I think the culprit might have been a dirty connection from the battery to the reg/rec.
Anyhow, the voltages were reading correctly last night after I put everything together again, and then I took it for a ride for 30-40 minutes and the battery recovered back up to around 13V after 20 minutes or so. 30 minutes was about how long it took in the past to drain the battery and leave me stranded somewhere...
Thanks a ton for all your help, I was definitely at the end of my rope there.
Cheers.