I don't know if this will help but I've attached 2 photos of my 78's stock quarters where they meet the crossmember. Note - with the sill removed they "fall" a bit and just touch the crossmember at the curves. Before, with the sill in place they just almost touched. The 4 body mounts at the sill/frame "push" the body/quarters up a bit off the crossmember with a tight fit.
I too am concerned about CCOT quality. Still up in the air on where to order my sill and a few other panels.
When I purchased my FJ40 the sill had already been replaced with 2X3 tube steel so I had no idea how the quarter panel was supposed to sit.
Does any have the distance from the top the rear crossmember to the top of the sill?