I remember reading that the internet settings may get hosed when flashing firmware but you can get them back by going to a page on SonyEricsson's website and filling in a form. The settings will be sent directly to your phone. I don't have the URL handy, but you can find it if you poke around these forums.
As for the applications, which applications are you talking about? The branded firmware will have different apps than the generic firmware, so this should perhaps not be surprising. What carrier was your phone branded with?