I tried the update/upgrade but it didnt fix the issue... So I started playing with packages and got it working.
Posde suggested removing asterisk-config, but it wasnt there to remove. So, I added it which removed all the pluto/asterisk packages. I confirmed the conf files now existed, then just re-installed the asterisk-pluto, pluto-asterisk, pluto-voicemail-monitor, and freepbx. After a reboot my trunk registered and all SIP phones connected.
I got the softphone working in seconds, but now I'm on to the SPA. I think I can receive calls, just not send yet. I should be able to figure it out with a little more searching.
Thanks for the help!