Sorry pal, I think your apps are down the drain. Apps2SD doesn't necessarily move the apps to the SD card so that if you plugin the sd card on any phone it would work automatically, your phone still has the data of what apps are installed.
If I'm correct at the assumption that you are now using a new ROM, your phone basically got reset. The best analogy I can think of is when you format a PC. When you install the OS, all the files in the drive are still there, but the System apps and files are all brand new.
What can you do in the future? I've heard good things about Titanium Backup, but personally I prefer Appmonster. It basically saves the APK file of an application installed so you can uninstall/install on your whim. Please do note that I've never used Titanium Backup, but from what I hear you can restore lots of things from that app: applications, SMS, Contacts. Not sure if it also saves the state of the apps and restores them to your phone though.
So I guess you need to download all your files again.
I went to the Play Store and looked at the Apps2SD app and yeah, it works as I have outlined above. I looked at Titanium Backup too and it claims it can backup your apps and data. Here's where it hurts though: you need root access to use it. Basically, the ideal way would have been to root your phone first, use Titanium Backup, then install the new rom.