Did you back up your /home/<user>/.mozilla folder (it's a hidden folder in your Home directory) first prior to installing Mint 9? Or at least, did you backup your Bookmarks separately (i.e. Bookmarks > Organize Bookmarks > Import and Backup > Backup), or have addons like Xmarks to save your bookmarks in an online server? You say you have a separate Home partition, but did you ensure that it was not overwritten or formatted during the installation?
Debian Testing x64/LM9 Main x64/Windows 7 x64 - LG R580 laptop w/ Intel Core 2 Duo T6500 2.1 GHz, 4 GB DDR2 RAM, Nvidia Geforce G 105M, Ralink rt2860 802.11n, 300 GB WD HD 5400 rpm