Good to hear. Glad everything worked out fine.
The Flash issue is an easy fix, and you can go about installing it in one of two ways.
1) Get the libflashplayer.so (32 or 64 bit) from Adobe's website and copy it to the ~/.mozzila/plugins/ folder and the /lib/ or /lib64/ folder (for 32 bit and 64 bit respectively).
2) Issue the command "sudo apt-get install ubuntu-restricted-extras", which will install Flash, Java, audio/video codecs, and some other things.
EDIT: Didn't see the issue with bookmarks. Not sure if there's a way to recover them now, but with the Ubuntu One Firefox plugin, you can sync your bookmarks across all your Ubuntu installations via the Ubuntu One cloud service.