I'm having this same issue. Did the new throttle body actually fix your problem?
I've had CPS and CKP replaced already after the new engine install. I have new plugs, plug wires and coil. Still stalls.

 

I have had the same issue a few times! The dealer said they could not duplicate the results and sent me on my way

 

Any updates?

 

I've have the same thing happen a hand full of times over the past year.. stock 08 6 speed with 48,000 miles. Very random but will happen as described at red lights.. everything fine one light.. the next it stutters and shutters but has never completely stalled. I'm at a loss as well being so random. hmmm

 

Yes I had the same happen to me today, half way across the intersection at low rev's and in 2nd gear and tried to floor it and it just died and went into splutter and shake mode with no throttle responce. It appears to be so gutless at low revs, are all JK'S like that ?

 

I had this problem, it was actually a vaccuum leak on mine...

 

Same with mine.