Ball python health questions

Question
Hello Kevin,

I was wondering if you could please answer a question or two about my ball python.  I believe it is perfectly healthy, but there are a couple things about my snake that I noticed, and out of curiosity I want to find out a bit more about them.  I don't know its age or gender, but she is about 20 inches long, and is able to feed on smaller sized mice.  I refer to the snake as a "her" but this is only because I named it a female name. I got her at PetSmart and she was hatched in captivity.  I use a douglas fir bedding, in a 55 gallon aquarium.  She has a warm hide, a water bowl big enough to soak in, and a hide on the cold side of the tank as well.
     Question 1) I have noticed areas on the snake's body that look a bit discolored.  The spots are a light brownish-tan color (almost the same color as the snake), but they're in the dark areas of it's body!  They are not simply normal color variations, but they almost have a bumpy look to them. I thought of scale rot, mites, ticks, etc., but that doesn't seem to fit the bill. I noticed a weird looking fly with a red head about the size of a fruit fly in the cage. I REALLY don't want parasites!  She had a difficult shed recently, too, so that may have played into things.  She still eats extremely readily.  The only behavior that I notice that's a little abnormal is that she seems to have developed a tendency to hide under her water bowl for extended periods of time, as opposed to staying under the warm shelter for most of the day. She's not as active at night either.  It is October 22nd right now, so maybe it's just a winter slowdown.  Any input would be appreciated.  Also, she has a few lighter colored scales running down the side of her spine, in a bit of a line shape. I'm probably just paranoid, but better safe than sorry.  Thanks for your help in advance!

Answer
You set up sounds good. Good job on giving plenty of info to answer your questions properly.

1. Okay, you only asked one question! You are paranoid. This sounds like normal variations. I do not think that the fly has anything to do with it. Depending on the size of the bumps and discolored scales, the bad shed could have something to do with it. Boost the humidity a little. BPs are prone to acting weird in the winter. I would not be alarmed at the hiding under the water dish. Shoot some pics of these "bumps" to me at lasher9@gmail.com and let me take a closer look just to be sure.