1) Okay. I recommend two things for the kernel:
a) Update to the latest stable version, which is 4.3.1 (or the beta, which is 4.3.2).
b) Try the less HAVS version, which should fix the screen tearing.
You can get the kernel of your choices (including the sbc version) here:
http://www.qap.la/~netarchy/
My guess is that will fix both issues.
2) What did you rename the nandroid to? Likely, that's your problem depending on how you renamed it. Do you have any other backups you can test?
3) Well, there's a difference between flashing a stock ROM and fully unrooting. Flashing a stock ROM is meant for those who just want to keep root, but want a ROM as close to stock as possible. Likely, the ROM will still have root permissions, and have some of the basics such as busybox. Also, you noticed the odexed and deodexed versions. Here's the difference:
a) Deodexed ROMs allow you to make changes to certain apks. The purpose is generally to theme. There are exceptions to this, most certainly, but if you want to flash any mod out there, you'll likely need a deodexed ROM. A *normal* stock ROM is not deodexed. Most custom ones are, and a few of the "stock" ones are provided in both formats.
b) If you intend to do no theming at all, and don't want to flash any mods that require a deodexed ROM, flash the odexed one. Why? Because it's faster.
This is not the same thing as unrooting. Unrooting will change S-OFF to S-ON (relock nand), replace your custom recovery with the stock one, change radio versions to match your hboot version if you ever updated them, and replace whatever ROM you may have with a completely stock one (all stock apps, i.e. bloatware, reinstalled, all personal data and apps uninstalled, all settings default, etc.).
