The thrust plate you made will not hold. Wood is not strong in the way you have loaded it - you need to use 3/4" plywood or a flange with nylon bushing.

To answer your question, the problems you're having are not common, but you've modified it so much it isn't really a Filastruder anymore.

The problem isn't the mounts, it is the thrust plate.

I have been having some troubles getting our Filastruder to extrude properly and I have a few questions and would like to see if anyone else is having these problems. Firstly, we destroyed a thrust bearing and pieces fell down into the barrel, causing damage to the auger and consequently bending the barrel. So, I ordered a new thrust bearing and washers, a new auger, and I bought a new barrel and re-machined the hopper infeed. Which brings up my first question, does it matter if the barrel that I bought is galvanized? I didn't even think of it at purchase, but could the zinc coating of the new barrel cause problems?
Also, we have had some misalignment issues with the motor shaft connected to the socket and the shaft of the auger. It seems to me that there is just too much pressure on the wooden mounts which hold the assembly in place and assist in alignment. So I re-machined some new mounts out of hard wood and reassembled the machine using metal brackets to secure the mounts, making sure it was aligned very well. Still, after about the first five minutes of my test run after that, the assembly pushed apart and caused misalignment. Is this common?
My next step is to again re-machine new wooden mounts, but secure them in dado joints cut into the baseplate, and also attach a "faceplate" on the front of the assembly with dado joints to try and strengthen it overall. Do you have any suggestions? I've attached pictures of the machine after my latest test run.