The nandriod should have put your apps back too as it is a complete image of your whole system.
You are using CWM, right? I have not used CWM in a long time, so it may be different then what I am using. Have you tried TWRP? You can get it though goo manager (in the market) then load it up, click menu, install openscript recovery and that will install TWRP for you.
After TWRP is installed, boot into recovery, make a backup
Lots of roms are set up to use TWRP now. I heard CWM has come problems and some roms do not flash right under CWM.