First, let me make sure I understand how the caller ID is working for you now. If you have the phone number in your contact as (555) 555-5555 W 123 you are saying that when that number calls you on the Storm2 the caller ID shows both the name and number. Is that correct and also you do not have that same telephone number listed in the contacts without the "W 123"?
If that is the case, what is the procedure for reloading the OS without losing my thrid party apps and all of my custom settings for all apps?
Follow the link below for an excellent tutorial on how to reload your os. It also goes through backing your bb up. As for 3rd party apps, I have always reloaded them individually. I might alos suggest downloading Smrtguard before you do anything. It's a free app that will allow you to backup your contacts, emails, phone log and calendars. Make sure you do a full backup with Smrtguard. You can find this at Mobile Security & Wireless Backup for Smartphones - SmrtGuard. When you reload the os, download smrtgurad again and do a full restore.
I just switched to the Storm 2 (work bb) 2 weeks ago and am still playing with it. So far I'm happy with the official os but will start playing with the hybrids soon. As for functionality, you shouldn't notice much of a difference, if any at all. I'm still using my bb so thats one of the reasons I haven't really started playing with the storm 2 as of yet.
To date, the only issue I've had is memory drain, and I've traced that to some themes I use. Once I got one I like, then my memory has become stable.