This is what I would do. Do a titanium backup of your stock rom once rooted. Takea copy of the whole backup folder from the sd card and store it somewhere safe.
When you flash custom roms, its best to ONLY restore using the following option:
"Restore missing apps with data". This will only restore user apps (YOUR apps) and their data. The reason this is good is because it doesnt restore incompatible system data. You will still need to be selective. Anything that looks like it is part of the rom (i.e not installed by you) you should unselect before doing this restore.
Its best to have contacts as google contacts as these wont be restored doing this. Nor will sms. I use sms backup+ to backup SMS to gmail. Its free and its cool.
Hope this helps.
Edit, forgot to say:
When you go back to RUU, make sure you backup your entire titanium folder to another safe place and resturn the original backup from your rom. You can restore all of this (except the super user app). Titanium needs root though, so google and download visionary+ to get temp root on your RUU's phone. Its lost at reboot.