I'm thinking the border was ruffley because you did not measure the border properly before applying. If you just try to sew a strip on as a border without measuring, chances are that the border fabric will stretch as you sew. This may not become obvious until you get a lot of the quilting done.
The way to correct this is to measure through the *middle* of the quilt. To add the side borders first, for example, measure through the middle of the quilt from top-to-bottom. Cut your two side borders to that measurement. Pin so that the border matches the edge (pin middle and ends first, then halfway between pins, etc. until entire border is pinned). Sew the border, easing as necessary. Then measure through the middle side-to-side to determine how to cut the top and bottom borders.
As long as you have enough free fabric at the edge, you can still attach a border to the top. It's not clear to me if you still have the batting and backing fabric to accommodate the borders. If not, you can piece additional batting to the existing batting (same with backing fabric). Once all 3 layers are there, you can pin and quilt the border as usual.