I would stay with my original quote, keep notes & accurate time involved & figure out why my estimate was so far off so I wouldn't make that mistake again.
One way to remedy this would be to come up with a formula And base your pricing on the quilt size and complexity of the design. Such as (72" x72" square quilt = 36 square feet. - simple piecing @ $5.00 square foot = $180; more complex piecing $8.00 sq. ft = $288; complex quilt with applique, custom quilting etc $12-$15 sq.ft = $432 - $540) this is just an example your own formula needs to work for you. Or, figure cost of materials, X 3 plus cost of quilting. Cost based on time is always difficult - you never know when something might cause it to take longer than anticipated and, if you are making a quilt you've made a dozen times you are probably much faster than the first times- so you are then under cutting yourself.