Okay everything is working great now all the apps are there. I answered my own questions. And Thanks OMJ you were right not having the SD card set up for apps2sd was the problem.
So here is how I fixed the problem just follow this guide to repartitioning your SD card. Oh i did this by simply putting the phone into disk drive mode no need to remove sd card as the guide says it works fine in disk drive mode.
SD card partitioning - XDA-Developers
I then downloaded the new super wipe script from here
So after you have set up your SD card go to recovery and run the super wipe script, then flash the new rom and everything is running great now.
Thanks again OMJ.