1. Media Manage didn't cause your problem, but in an emergency to download, install and use Desktop Manager, you don't need the bulk of Media Manager. Plus you really don't need it in the long run.
2. You choose. Simply personal. If it were vital, I would go with 4.2 for now.
3. Sorry, I missed Jibi's post above. You can use that link he gave you, for instructions for your issue also.
or this:
How do I wipe the BlackBerry using Jl Cmder? - BlackBerryFAQ