Wow - 12 pages. I missed a lot.
As to the science side, we all agree that pressure is directly related to temperature via the ideal gas law. However, units of measurement matter.
Edit: I had a sort of long winded response written, only to find an article that covered it with Pascal and Kelvin as the units of measurement.
Deflate-Gate: Could weather have played a role in deflated balls? They find that the balls could have been deflated by as much as 0.7psi based on temperature and atmospheric conditions.
Again, it didn't matter in the game. SB49 will highlight the two best teams in the league. The refs may not have checked the pressure before the game appropriately, the ball-boy may have let some air out in the bathroom - we don't know (see, I'm just like Tom Brady).
Oh, and as to the low total fine amount - keep in mind the company Goodell and Craft keep.