The portion of the airflow that is to the right of the stack in your pics doesn't look like it will have a straight shot to the stack unless the stack is a lot shorter. Can you cut the stack to make it shorter? That would avoid a lot of "machine" work on the plastic parts.
I don't think the position of the filter will have much effect on flow but it certainly would be a lot easier to R&R if it were in the original position.
Hang in there! This is one of the few time I'm hoping someone proves me wrong.
