This is why I never jailbreak; never want to go through the hassle of backing up individually, re-jailbreak, re-install, etc, but this is off topic
Ah, but the many hundreds of additional features my iPad has due to being jailbroken is
well worth the 15 minute process you described. It's not like i'm getting a new device every day.
On topic: Sounds like you have it right OP, but I have a warning for you. Both aptbackup and pkgbackup have not been updated for quite a while, they are known to have problems on later iOS versions (such as 5.1.1). I would still suggest using them, as they make the process
so much quicker, but I would also suggest getting an old fashioned pen and paper and writing down each tweak, repo, and any specific settings for any of those tweaks. Trust me, if the backup app screws up, you'll be glad you took the 10 minutes to do it, otherwise you'll be hitting yourself as you rack your brain for everything you can remember.
Edit: Oh oh oh, and when you use aptbackup, be sure to transfer the file off of your device over SSH or other means (and make sure you write down the directory you got it from, cause you will most likely have to put to back in that spot on your new device). Otherwise you are basically making the backup and putting it on your device, then giving away the device with the backup. And before restoring, go to settings>general>reset>erase all content and settings, then restore in iTunes. This will ensure absolutely all data, jailbroken and unjailbroken, is off the device. But be sure to do this only after you have transfered the aptbackup file to another computer, or it will be deleted as well.