I purchased a like-new (or so the previous owner said....) Rev 3 and have been absolutely perplexed as to why the shock’s top mounting will not accept the mounting plate and why the mounting plate will no longer accept the shock bolt?  Unbelievably frustrating as I cannot imagine a more straight-forward procedure...remove shock, replace shock only now it absolutely refuses to fit!  Photos attached for reference. 

Thanks in advance for any suggestions - 

I had a 2001 model and a 2002 Beta 250s back when they where new, i remember upgrading the 2001 model to the newer 2002 airbox. I had to take a file and take out a small amount of the aluminum frame to fit the 2002 rear stays in.