Sideways....
I have never heard or ever seen a flywheel cause this kind of problem. Even during my drag racing days. The rear main may have been starved from oil and overheated, then the crank warped. The bearing does not have to spin and that's a huge plus. Let us know what all you did and what you spent. I'm curious how each tackles this problem of rebuilding a flat 6 and how they may cut a corner to save a few bucks. By the way, what year is the Boxster and what did you get it for $$$$$.
PS. Maybe you should do the assembling in your living room. Built a Lotus engine one time like that.