Where are you measuring the length of the borders. You should be measuring at the center of the top and maybe either side to get the length of the borders. This is the measurement that you should use for the borders. If you are adding cornerstones then make the main border smaller by the width of the other border for the cornerstone. Just measure the width of the inside of the top not including the side borders. Then add the cornerstone that is the width of the border. this should fit the top.
You should not just sew the borders to the side of the top and then cut off the excess border since te sides of the top may stretch and each side of the top may be different.
To add borders- Measure the INSIDE of the top and cut both borders the same length using this measurement. Fold the border and the top in half and quarters and then pin these sections together. If ther is a difference then ease the extra fabric into the other top/border. This method assures that the quilt will be even on the sides. should prevent wavy borders.