Iceblossom

I'm not sure if I'm quite following what the issue is.

You have two sides that are correct/the same, and two sides that aren't. Is the quilt square or rectangular? How big is it, it's one thing fitting in an inch over 60 inches, and another thing over 36... You might be able to put a simple gather stitch in (or use lots of pins) to take up extra fabric, obviously if the problem is not enough fabric you would have to do it differently.

One of the things we do when things aren't going together perfectly is to frame the fabric in some way, so you have the appearance of consistency/squareness for the finished project. So you put on an inner border to make the sizes consistent and make your math work out. Your eye won't notice so much if the top is slightly skewed, and your final border should carry the design. Bonnie Hunter uses a narrow inner border a lot to change the math from the body of a quilt set on point, to a border set straight.

On my latest Bonnie Hunter project, I was using my newish machine and my seam allowances are way too scant. I had an extra 2" I think by the time I was done. Lucky for me, I was also scant on my border units and it all went together super easy just by luck and chance.

Or, here's the good enough side of things. For years I didn't really care so much if my tops were slightly out of square -- the only time you notice it is when you try to fold it. I would put my sides on "as built", to the fit of my final project. OK, so I find I like my results better if I square them up so now I do measure and cut both sides the same, and the top and bottom the same and fit in the top to those measurements. It being out of square does not keep me awake at night, so long as I am warm enough to sleep!