i would encourage you to do more research in the future before you begin making such drastic changes to your Phone. First thing you need is Koush's Bootstrap recovery app. It is available in the market for $2. This will allow you to access a custom recovery mode different than the one that comes stock on the phone. Here you can make (Nandroid) backups of your entire phone. (It occurred to me you must have bootstrapped to clockworkmod recovery to have installed apex) So next time make a backup of your phone before installing a new ROM. I think the apps you are looking for that you "did not get back" are Blur apps. Motorblur is the stock User Interface that comes with the phone. Apex allows you to get some of these back from the apex toolbox. i would suggest that if you like the Blur apps to not load custom ROM's because one of the goals of most customs Rom's is to remove as much blur as possible. I personally enjoy apex because i can still access the parts of blur I like. i.e the alarm clock. I have never SBF'd but can at least tell you to make a backup of your current Phone settings before you try anything else.
