I remember having the same issues with my RPM. I used a drop base air cleaner and a 3" element with maybe 1/2" clearance. I had solid motor mounts made. You can go with the smaller element. If you were to see the pancake air cleaner Pontiac installed on the 400, and the size of that element, 2" will be marginal with a stroker.

There are a few air cleaner bases from later Pontiac that will work, just have to search the archives for the exact applications. Mine, I believe was an older Moroso base/lid.