Does using the lover stone prevent you from getting the rested, well rested, or lover's comfort bonus?

Not to my knowledge. Those usually stack

(null)

I believe that it does. I haven't gotten any of these bonuses since I activated the Lover Stone. You could always do a test and activate a different stone and then sleep and see what happens.

The Lover's Stone effectively applies a permanent Well Rested effect to the character (15% magnitude), so no, they don't stack.

I can get both. Sometimes when activating the stone lovers comfort goes away. You can fix this by sending you wife to her original home and then sleeping there. After that you can send her back to your house and lovers comfort will now work.