Your temps are too low for starters. The warm side should be 90-92F and cool side should be 80-85F. As for humidity it should be around 60%. This could be caused by low humidity or dehydration. If there is a large bowl of water in her cage and her skin is not wrinkled I doubt that she is dehydrated. What kind of substrate are you using. Best substrate for humidity is coconut husk or cypress mulch. I suggest you get sphagnum moss and place it all around her tank and in her hides to up humidity. Cracked eye caps will not heal per-say. It will take a few sheds for the eye caps to get back to normal. Which means keeping the humidity up for then next few months. During this period it may be best to stick her in a tub enclosure where humidity can be controlled a little easier. It is always good to have a back up "medical" tub container anyway just in case something is wrong in the tank such as mites or an RI.

The whistling is very common especially when handling. If your ball python starts making popping noises, then you should be concerned but not with whistling.