Ok my car is past the basic warranty. I have a Prem Care ESP for my MKS though. I understand few things like software changes and updates (With exception of APIM/SYNC, Under extended warranty) are not covered under even the premium care. So if a module (Like FCIM or Cluster) just needs a software update to repair a concern It's out of pocket. However, if the problem is covered under a TSB, Does that change anything?

No.  Warranty coverage is the important issue (whether B2B, ESP, or extended warranty from Ford for special items).  TSB is simply a service bulletin that acknowledges an issue exists, and how to resolve it, officially.

Never very sure what will be covered under warranty work or not. For example, the other day, I was having some minor shuddering. They updated the Transmission software or something like that and told me it was covered. This surprised me since you read the paperwork and it says software updates and calibrations aren't covered. So I wasn't sure if TSB's had an effect or not. I am actually kinda new to warranties on cars, everything else I have ever purchased was way passed warranty and I worked on it myself. But this AWD beast scares me mechanically and electronically wise.

Too true.  Each dealer does things their own way.  The better ones will do stuff like this for their customers.

I've been to multiple dealers with my ESP and they have all said software updates are covered. I actually just got my APIM module reprogrammed today and they said it was covered by itself.

Nice