I don't think I understand what the issue is.
Are ALL your NPCs missing or custom ones you want to add?
If ALL NPCs fail to appear then this can occur due to client version mismatch (I came across this issue on eA by another user). Make sure your X-Ray client matches packet version with your server settings. I recommend you try a packet V8 client just to figure out if this really is causing the problem.
If only custom ones are missing the post the related configuration files please.
Regarding patching, I recommend you check out the Thor Patcher. Go
here and search for the Thor Patcher.
Regards,
Mercury