Use the Transfer Multiple Accounts. We had to move 100 customers last month from one DC to another due to problems with the provider. We lowered the refresh time 48 hours prior to the move then just transferred all accounts from one server to the next. There will always be a couple that might have a configuration error, but the whole process only took a couple of hours and that included sorting out the bugs. The new copy scripts really work well. They will bring all current email, cpanel configs, DBs and everything else in the users account. It takes some time, but it works well now. My only suggestion is make sure your are up to date on the release you are using and make sure the WHM releases match on the two servers. We use Current on all of our servers, except for this last update that is broken, and rarely run into any issues.