I really enjoyed reading this Adam. After 4 years working from home for most of the time I can see my weak points and strengths very well defined in your post. I totally agree with waking up naturally (no alarm) and my trick for that is complete lack of curtains in the bedroom. I started this "technique" of mine few years ago, and it is one of the best things I ever did. I find my perfect time around 7am, I can even do 6am sometimes... but 8am is the winner most of the time :-)
My other little trick is no TV and when I want to watch a movie I use the Mac. No TV is a blessing... believe me :-)
I also find gardening a great way to get away from the computer and get a bit of fresh air.
But if there is a piece of advice I would give to anybody working from home and self-employed is to avoid the "news" as much as possible. And when I say "news" I'm talking about all those stories of disasters, crisis, more crisis ad more crisis... focus your energy in solutions... no problems :-)