IF it lays flat - and seems reasonably straight - I, too, would layer it, baste or pin it securely and quilt it and go from there.
One can ease in 3/8 of an inch pretty easily over 54 inches of length.
However, if it's really bumpy/puffy/ruffly in just one or two spots, I would probably try to figure out why it was that way and do what I could to correct it before going further.
It is a pain to redo a block, but it really is worth it in the long run.