3" is an awful lot of excess fabric so I would try and fix the issue. You say once all your borders were off the quilt it is still out of square (has a waffle as you put it). Is it still as drastic as it was (3" of excess fabric) or did the problem get worse with each successive border? When you measure each side of the quilt how far off are the measurements? If not much (say 1/2" to 1") you can ease those in by measuring through the center of your quilt for length and width and cutting your border to that measurement, pin a lot and ease in that excess. Repeat the measure and cut to measurement for each successive border. Usually this problem rears its ugly head when you don't measure for your border, just take a long strip of fabric and sew it and cutting it even with the quilt's edge. Often referred to as a slap and sew border. If you plan on having the quilt longarmed you will need to get the waffle out. It won't present as much of a problem if you plan on quilting it on your domestic machine but could still result in a wrinkle or pleat somewhere.