First, consider a backup strategy such that you always have one set off line, that means two backup sets minimum.
A combination for some is to clone their system weekly and use TimeMachine (though I am more inclined to change backup schedule to one or twice a day, only when the system is idle, and other things).
And keep all the original software installers on a non-system drive too.
You should have with a clean install of the OS not had any 3rd party or issues unless on backup drives.
I don't know if you can selectively restore with what you have or used. Carbon Copy Cloner backups are very flexible.
http://www.macupdate.com/app/mac/13635/vuze
One thing to remember, P2P means your IP was/is out there, and there are going to be more denial of service, rlogin and other queries at your front door (modem or router firewall).
It uses Java, has a Firefox plug-in. To use all its features, you do need to do some configuring, nothing as bad as RedRyder or White Knight even use to be, but more than average for most.
http://azureus.sourceforge.net/
http://wiki.vuze.com/w/User_Guide