Im on firmware 3.1.2 and I am 98% sure that I have an untethered jailbreak with Blackrain. If I upgrade to 3.1.3 and jailbreak using Sprit, will I have to restore my phone?
If you have an untethered jailbreak, and you really want 3.1.3, then restore to a custom 3.1.3. Spirit is really meant for people who were tethered or not jailbroken at all.
Yes. Honestly, I'd recommend just staying where you are. Very few apps require 3.1.3, and there are no real bug fixes other than that battery display issue. And I'm not even sure that was a real issue.