If you're satisfied with how it looks (except for the waviness), you could measure down the center of your top to get the measurement for your border. I usually measure through the center then measure a couple other places (not the edges) and figure the average measurement of the 3 measurements. Then when you attach the borders, have the wavy part down towards the feeddogs when sewing the borders on. You can kind of pull on the border so the feeddogs "work in" the extra fabric.
After doing the 2 side borders, do the same measuring and averaging the numbers and sewing with the waviness toward the feeddogs. This waviness thing happens to me a lot and by the time the quilt is quilted, it's fine. I have to admit I usually don't square blocks as I go along because I don't want to cut off any points on my blocks.