What I do with the threads is this: when you cut the threads, leave long tails (about 4"). By hand, use a sewing needle to thread the top thread down to the bottom. Tie the 2 (now both on the bottom) together with one knot. Then use the sewing needle to thread the tails into the middle of the quilt and away from the knot as far as you can. Tug on the thread a little so that when you clip the tails off, they will hide into the fabric.
As for quilting the border, I think if you X stitch in the 9-block patches, that the border would look great with a meandering stitching in the John Deer border.
Nice quilt...my nephew would love it.