Receive Shadows from Surfaces is still enabled in the *cloud layer* in this file. That is likely responsible for the high render times. However on my machine (a fairly modest-by-modern-standards i7-2700k at 4.2Ghz) it only takes 15 minutes, nowhere near the 3 hours you said it took you. I'm fairly sure you have a similar or better machine than mine so something may be going wrong on your machine. Any thoughts what it might be?
- Oshyan