I fitted a RH torque box to my '67 FB & it fitted up with no dramas whatsoever. I don't know why yours is a poor fit - again have you got the right one, a mirror image to your original LH one?
I just made sure I painted & rust-proofed the interior faces of mine before I had it welded in, & the floorpan, because you can't adequately get to it all afterwards. You seem to be doing all of that type of work with great diligence.
Don't be discouraged, yes much of the work you're doing now is hidden later. But YOU know that it's all being done correctly, & that there couldn't possibly be any re-work required down the track. You're doing more than Ford ever cared to do.