How discouraging that must be - have you tried steaming the sides really well? Lay out the quilt flat so that you can hand press the wavey parts as flat as you can make them, then steam them really well and when cool enough for you to touch, hand press them again to get it really flat and even. then you can put a strip of painter's tape on the flattened fabric just inside the edge...far enough inside so that you can do a hand basting stitch around the edge of the fabric to keep it flat and even. When the hand basting is done in each area you can then gently remove the painter's tape and move on to another section of the quilt. Move around the quilt a you do this to get all of the edge done. The hand basting on the edge will hold it in place until you're done with the quilting and ready for the binding...