The fag pad helps protect the block from hitting the crossmember with stock mounts. I've personally never seen a block hit the crossmember, regardless. I removed mine to permit clearance of the BB DET motor/oil pans. With Poly mounts, you're more than safe.
(For the record, the "pad" is actually like a mild steel, not rubber like I had first thought.) I don't know how it would help protect anything at all. Just yank it out.
And I do have a 2 piece 2.25" MR header, that I don't know what to do with
It's been sitting in my garage since I went turbo the first time.