I was able to fix it. Those pieces sit up against the inside of the filter, some sort of a stop i'm guessing. Freaked out when I first saw them sitting in there like that.
New motor installed (3rd one now) from Airdog. It was popping fuses, probably from the blockage from the filter and the pieces.
One thing that needs to be noted is that Airdog uses a different motor now than the two I have. Josh @ pureflow sent me the new one and said he did not need a core back like usual.. and stated that they fixed all of their problematic issues.
This one primed like it should have right as I popped it in and cracked the filter, unlike my last two.
It sounds entirely different now than the other two as well. Josh said I wouldn't have any problems, we will see though. If not, I still have a backup behind my seat