Finally we have AS3 API, so I'll be implementing it today/tomorrow (scores will wipe again I'm afraid).
Also SCGMD3 should be coming early next year. It's mainly just more songs to kill your time playing.
It takes a lot of time to rig up a song, and if I did replace the songs only a couple of websites would actually replace the file (16 song version is still all over the place) so the effort really wouldn't be worth it.
I'd be better off making a new game. (Not that I am)
Check the game description for a guide to get your scores back, I had no idea Kongregate stored games on their server in such a way that updating it would mess the scores up. Your lag is nothing to do with the new version.