Ha, if only manufacturers would be as good as the community with their roms. The only one that does a good job is Motorola (and Oppo, as it's supporting CyanogenMod officially). HTC and Sony do a decent-ish job, and Samsung is usually the worst.
I'd say do your homework and then flash. That's what I always do (when I bought my Nexus 7, I didn't even boot into stock. It went straight to CyanogenMod).
About the rom, I usually suggest CyanogenMod because it's the one that feel more polished, has more official support and actually include features that I care for (Location tracking without having to rely on Google, Secure SMS between CM users out of the box, permission management like iOS) instead of trowing everything into the mix. Other roms that I like are Omnirom (still in development so it's still missing some features, but it's good enough) and Slimkat. I'd advice against running nightly images, because you never know what could break (I use the CM Milestone releases), but usually those are mostly fine.
The only exception here is about the Samsung Notes, since AOSP doesn't support the S-Pen as good as stock. The situation is improving, but for now I'd still recommend to flash a rom based on stock (which are usually still miles better than stock).
Regarding your issues, it's a well-known fact that you should always do a full format when switching between roms (especially if they are on a different version and base), even your applications data. If you need some data backupped, there are some applications that can do a backup/restore for you (Helium comes to mind).
As for the recovery, you've flashed CWM which is fine, but I usually suggest TWRP since it's opensource and has more features. It's also the one supported by CyanDelta/OpenDelta, which allow you to quickly upgrade your rom.
And for warranty, you can always flash back to stock
Only the Galaxy S4/S5 have an hardware check that you can't revert back (and some phones require you to ask for a code to unlock the bootloader, and so voiding your warranty).
Oh, and XDA is terrible. It's the place to go, but still terrible. I don't know why there isn't a better alternative yet.
And obviously don't flash unless you're prepared to buy a replacement phone just in case something goes horribly wrong!
It's pretty much impossible to **** up an Android phone. If you break the system (which is pretty hard as well) you can always boot into the recovery and format/flash again. If you break the recovery (I'm not sure how one could), you can boot into the bootloader and flash a new recovery.
Also first posts on the forum, so I guess hi everyone.