So here is the story:
I had be putting off the upgrade of asterisk, mainly because I was going to have to build it from source.
To make a long story short, 20 hours later, I get everything back to normal, well I thought so - until I tried out one of my voice menus It sounded about like I was talking across the world on a old CB radio!
That was on the TDM-400P,
I proceeded to try out my softphone which had the same results.
One clean reinstall later, asterisk was not working any better.
Next I tried Zoiper with IAX, which worked fine!
Finally I found, that if I was using GSM as my codec every thing worked fine on SIP or IAX.
But that still leaves my TDM400 not working:(
If any one has any ideas on how to get asterisk working better, please let me know!