Unfortunately (?) my car does have the crossmember shims in place and does not have floor damage.

Finally decided to tweak the header pipe. Took pipe off, filled it with sand using a lot of tapping to get it to pack down. Ends of pipe were plugged with wads of newspaper tamped tightly in place.

Made a measurment tool to check bend progress by marking a spot on the floor next to a wall for the flange at the engine end and a mark up on the wall for the cat end.

Used my Harbor Freight 12 ton press with soft wood blocks on both sides of the header and made a couple of presses resulting in a bend increase of 1/2" at the cat end of the header. The sand and the wood blocks prevented the pipe from collapsing.

Removed newspaper and sand and reinstalled the header. Now the clearance matches that on my other two 240s (roughly 1/2" at the closest points).