3 inches is a BIG difference and will most likely quite noticeable and difficult to fix without ripping....you definitely want to get fixed before quilting as ripples are a nightmare to quilt, LA or fmq.....I would take off the borders, then measure top to bottom in several places, specially in the middle....then do the same side to side.....this will give you an idea if the problem is in the pieced top or the borders.....also measure the individual blocks to make sure all are the same.....as posted before, cut borders to length specified in pattern......I like the pieced borders, but make sure you are keeping the little blocks all the same size after piecing together....bias edges can be a pain to work with, but starch will help.....good luck with the fix, the quilt is very pretty and worth the effort!