Okay, I'm thinking someone'll be able to help with this.
I'm looking at ways to speed up my 4.1.1 Nexus S which is getting a little laggy as of late. It's all rooted and the like but I'd really like to get it to run a little smoother and faster except I have no idea what methods or evenROMs, kernels etc. might be suited. I'm fine with doing a factory reset as long as I can restore app saves and settings etc. and admittedly I don't really know how to do that either since I didn't have any problem with deleting stuff when I was unlocking the bootloader. Any ideas?
Use Titanium Back up to back up your save files. I ended up purchasing the full version because I of how much I use it, but free should be good enough. You'll want to do this because you're going to be doing a clean wipe which wipes out all the data and settings (but it doens't wipe your photos/other downloaded files).
I'm assuming that you have use have a custom recovery like CWM or TWRP
I've been using TWRP:
http://teamw.in/project/twrp2/44
Use the 'Android App Install Method (Preferred)' if you want.
For backing up text messages, I use:
https://play.google.com/store/apps/details?id=com.riteshsahu.SMSBackupRestore&hl=en
In terms of roms:
Codename Android is great for a ton features/customization and has been stable on my Galaxy Nexus:
http://codenameandroid.com/forum/index.php?/topic/174-codename-android-350/
If you are looking for something that's pretty much stock there are roms like Bugless Beast. Just make sure that you are flashing the right version of the rom because there are multiple Nexus S's (a GSM version, which I'm assuming you have and the Nexus 4G). The links I gave you were to Nexus GSM versions of the these roms.
Whether you use TWRP or CWM as your recovery, the typically steps are:
1. Factory reset (deletes all data/settings)
2. Flash the ROM
3. Flash an updated GAPPS (usually provided by the developer of the ROM)
4. Flash kernel
For the Nexus S, I honestly don't know the best kernel for this phone. I think a lot of people like the Air kernel:
http://forum.xda-developers.com/showthread.php?t=1469842
Or just check the XDA page out. There's a lot to choose from:
http://forum.xda-developers.com/forumdisplay.php?f=883