I know that many have posted about the #2 cylinder head issue and thanks to that I got mine fixed. I ran into my problem I think in an unusual way from the norm and thought I'd share the saga.
(2012 Freedom Edition JKU with 12,000 miles, frame date July 2012, Engine date, (unable to find date on bottom of engine))

Brought the JK in 3 weeks ago for luke warm heat. (not so nice in the winter)

Symptoms:
-Low Coolant in reservoir (which I had recently filled)
-Luke warm heat output

They changed the Thermostat, and said it got worse.

Then they flushed the coolant system, said it was good to go and gave it back to me.


A week later the heat was pretty weak still my coolant reservoir was empty again after I picked it up half full.
Brought it back to the stealer-ship and and told them I believed it was the #2 cylinder head after reading up on the forum.

Symptoms:
-Low Coolant in reservoir
-Luke warm heat output
- Left side engine ticking.
-They say they saw steam in the exhaust. (kinda hard to tell in winter)
- NO, NONE, NADA Check engine light!!!

They stated it was the cylinder head. Had a 50% lead and a #2 cylinder misfire
Remedy: Replaced the left side cylinder head. and Radiator stating that it was cool on the bottom and hot on the top.



Its been 4 days since I picked it up. The divers side heat is like warm again!!!!! but the passengers side is roasty toasty. Guess ill be bringing it back again.


Other mentionables: They FIXED THE RECALL right again. Also reprogrammed the SLOW CLOCK ISSUE but didn't have my second key and didn't mention it wouldn't work. So that had to go back to the dealership to get the second key reprogrammed after I found out it wasn't useable as I was trying to go to work in the morning. They also never reset the clock to the correct time, BOTH TIMES (come on attention to detail counts). and they keep adding dealership license plate frames. Which I will continue to throw away.

 

Just played with a Thermal Immaging Camera at work and here is what I came up with for temperatures after the two fixes.

Drivers Side Pass Side
91 109 127 114
Floor
80 110

Degrees Fahrenheit

 

The heater issue has been solved by MULTIPLE heater core flushes in a single trip. A guy was having a similar issue, broke down, and flushed his own system multiple times and hasn't had an issue since. The issue was sand from the casting in the core. It took a few flushes to get it all out.

 

verify the heater core is getting proper flow. There are two heater hoses that go in and come out your firewall by the back of the engine. they should feel or read almost the same temp whether you touch it by hand or go by a temp gun. if theres a relative difference then you know it has to do with the flow of the heater core whether its blocked up or leaking. I have always done this by touch but then again I have been in the field for years.