Welcome to the site from East Tennessee. Sorry about the paint issues but glad the dealer jumped right into the corrective actions (as they should). As some others have mentioned, please post a couple pics of the scoot when you get a chance (and get it back). As for as the handling issues, I've owned many variations of the Electra Glide over the years (most recently an 09 SG and now a '12 SESG) and have never noticed anything unstable about any of them. Know a couple folks that have the new '13 SEEG and no issues with them, either. When you get it back and still doesn't feel right, let the dealer know. They may use the line "it's suppose to feel that way" or "they all do that" or "nothing wrong, it's in spec" BUT they may find something wrong so doesn't hurt to check.
As far as the site, it's a great place to get all kinds of opinions on your issues along with just about everything else CVO related. So enjoy the site, the new CVO (when you get it back) and keep it between the ditches...