I applied the beading last, handstitching it down over the gathered side seam. I finished the seams on my serger, and also serged a blind-stitched hem. The fabric behaved beautifully on both the industrial straight stitch and the serger.
I got a lot of compliments on the dress, and spent about $130 total on the materials. The fabric is so much nicer than the original dress, it feels substantial and has a lot less sheen. The gathers don't lay as flat as the jersey though, and if the fabric were any stiffer I don't think they would have worked at all. But I'm happy I was able to anticipate the differences and make allowances for them.