I have a 2010 Tc with a WR S/W Intake and I don't think mine sits like its supposed to. Also I took the filter off this weekend and used the cleaning soloution/warm water/bucket method and it turned out it wasn't that dirty. So I reinstalled the filter and now on my scanguage 2 I'm getting I/A temps of 89-128 at idle when its 55 degrees outside. Before I was getting temp readings about 10 degrees of the outside temperature. Any Ideas. I did wait 24 hours for the filter to dry out and made sure it wasn't wet before reinstalling.

This is how my intake sits now.

 

I have the same excact intake there is a metal bracket that came with the intake. Mines sits lower then what I see in the picture. I just bent the metal bracket to where I felt the Intake was sitting "Comfortably" as far for the temp reading I have no clue.

Did you disconnect the negetive on the battery to reset the ECU?
Let the car idle for about 10-15mins after the install?