Let me start by saying that this may not work for everyone, but it did fix my issues so I figured I would share it in hopes that it might work for others.

I too had been having most of the same issues as others, i.e. no audio, missing modules, stand alone and plug-ins crashing.

My setup is as follows:
Mac Pro 2.66 GHz Quad Core with 8 Gig of Ram
Mac OS Snow Leopard
Logic 9
Alesis Multimix 8 firewire
iLok

I had originally installed PodFarm 2.5 as a clean install being as this was the first time I had purchased anything from Line6. With that not working I had downgraded to V2.02 but was still having glitches however I was able to get some sound using the plug-ins in Logic. I decided to install 2.51 and everything crashed to the point where I couldn't open a Logic session if I had used a PodFarm plug-in on it.

This morning I decided to completely remove PodFarm, as per the instructions, again. This time though when I went to do a new install I choose to download PodFarm Version 2.0 and install that first. I did a custom install choosing only the plug-ins and the stand alone. I unchecked Line6 Monkey, License Manager, Audio Driver, Midi Driver, and Driver Installer.

Now due to my setup, I knew the PodFarm Stand Alone App would not see my Alesis multimix which was fine as I am more interested in using the plug-ins. When I fired up the plug-ins in Logic I had audio and was able to load the different presets and it didn't crash.

I then decided to do the same installation using Version 2.01, plug-ins, elements plug-ins, Application and Audio/Midi Preferences only. Tested again and everything was working minus the Stand Alone App not seeing the Alesis.

I repeated the same steps with PodFarm 2.02 and then with 2.51 with the same results except that Version 2.51 does see my Alesis MultiMix. So far what I need to work does work. Once again, I do not know if this will fix everyone's issue but it did fix mine.