Blocking out the sides is usually done when the snake is very shy and not eating. If Mycroft is eating just fine, then blocking it out is up to you.
With the whistling, check for stuck shed. As stated watch for mucous, as could be RI. One other possibility, is Mycroft very young? Is he breathing really heavy when he does it? Sometimes the little ones get stressed and breath really hard.
As far as hides, those half logs are horrible for bps. Thats why he never uses it. I would ditch it, and get a second identical hide. I wouldn't worry to much about it being cluttered in the tank. Especially if he is small, as small and cluttered provides security for him. How big is Mycroft? If you are worried, post a picture of him and his set up for us to see.
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