You will be surprised just how much you can see in 3 hours... especially if you are your own tour guide.
When I was there last year, they had closed the inside passages on El Castillo.
The majority of the items you have listed are in one general area. It is not at all difficult to walk to each item. I strongly suggest that you do go out to the Nunnary, and Observatory. They were wonderful to see, and in reality were not a long walk.
I have never made it over to sacred cenote, only because I have been told there is not much to see, however, this could be wrong.
If you are dedicated to seeing as much as you can, I don't doubt you will accomplish a lot in three hours.