I'm not so sure that the squeaking noise is related to my firewall flexing or welds failing because if that was the case my clutch would be squeaking all the time. However my clutch only starts to squeak after I drive it in stop and go traffic or I'm engaging/disengaging the clutch for a bit of time.
Because of this I'm thinking it could be the throw out bearing? Is it possible that after stressing it for a period of time it starts to squeak? I'm not sure if it's true but I always get the feeling that after my clutch starts to squeak it's harder to engage the clutch smoothly... It's almost as if the catch point is moving making me have to slip the clutch more. When the clutch doesn't squeak my clutch grabs fine.
I'm not too sure about the red flagging thing either but I've heard from people that once your VIN is flagged it's automatically brought up from any dealership whenever they try and do any warranty work. Apparently it's in SOA's database of cars? Not sure if this is true but if anyone knows more about how warranty work can be denied I'd love to get more information on it.