I am sorry that you are having a problem. Very frustrating.
You could do any of the things you suggested.
If the complete width of the border is not critical to the design of your quilt, I would probably just cut off 1/4 inch all the way around and not worry about it.
If the complete width of the border of the design is critical to the design, I would just put on a wider than average binding. My "normal" binding is almost 1/2 inch and looks quite respectable. (Start with a 3 inch wide binding and do some testing/practicing on similar sandwiches to get it a "perfect" width for your set up.)
Or you could trim 1/8 inch all the way around the quilt sandwich and make the border a teeny bit wider than usual.