At bare minimum you should be wiping cache partition & dalvik cache. Most recommend a full data wipe, but some like to avoid this because it causes you to loose all your data (like a factory reset). This is known as a dirty wipe or dirty flash. It works most of the time but can have ill effects afterwards.
Why your loosing the notification bar I'm not really sure.
1. Do your wipes.
2. Flash the ROM & GAPPS (if required) before leaving recovery
3. Do a boot up and shutdown before making any other changes by means of flashing mods, kernels, etc.
4. Any mods or themes you flash over the top of existing ROM, MUST be compatible with that ROM or things like the notification bar and other strange things can occur.
5. Since there are 3 versions of GNex out there.. Verizon's GNex/GSM (TMobile/AT &T and International) and now Sprint's GNex make sure your flashing the correct ROM/kernels/themes/mods for your device. Sometimes devs don't do the best job at clearly marking which download is for which device.