I was taught by teachers whom have many patterns and books to square up after the boarder was added if it needed to be squared. Never trim the blocks as you will lose the points or what is needed for yout 1/4" seam allowance. If your quilt was that far off before adding the boarder then find which blocks were causing the problem and fix them. The first quilt I ever made many years ago under these teachers was a nine patch and a flying greese, points had to meet up or you pulled out the seam ripper and re-sew the block. To make sure your cutting (use the same brand of ruler in the quilt/blocks, never trust or use the mats lines), seam allowance were right 1/4" and you were butting up seams when sewing the blocks. This has paid off I rarely have to square up my boarders or have problems now.
Are your wavy boarder due to the fabric stretching on the ends after being handled? I fine even some of the so called best fabric is awful this is where the walking foot really helps eases and smooths out