If you already have a titanium backup, I wouldnt worry about the apps. And as long as you have a previous nandroid or clockwork back up of your previous rom you should be sitting pretty. But not to worry, Just back up everything you can and start fresh. The reason I use Titanium is that it will restore the market links to the apps when I reinstall from a backup, I dont know if any other method does that.
What's the difference between a nandroid and a clockwork backup. When you flash a new rom (using ROM manager) and it asks if you want to backup is that enough? I also have titanium backup for apps.
I still get some forecloses (with helix2) and some freeze/lag when switching between apps and so would like to flash the cyan v.7 again but this time wiping data and cache to see if that helps. So, can I just hit backup ROM before I flash it again?
Thanks for all the help people have been generously offering! Its nice to see such a supportive community!