ActionVR
You're very welcome, as Conor said it is something that will start to get better as you fix the problems, from my experience it's something that everyone has had to deal with at the beginning!
The shutdown does sound very odd, you'll find an odd issue with shutting down is that SteamVR will prevent a proper shut down, I am in the habit now of turning off SteamVR before shutting down the computer each night which has fixed the issues. I am at a point where I shut down fully each night and turn on each morning very easily.
Are you using Wake On Lan to turn on your computers? And are you using any remote access software for your computers? These two things will make your life a lot easier as will learning how to setup some basic AutoHotKeys. Also with the Base Stations don't bother turning them off at all, there are plenty of operators who have had them running for years non-stop without any problems, I've had mine running almost non-stop the last year without any hassles as well, I actually recommend turning off the Power Management options (Especially the bluetooth) as this causes the biggest problems for people in the past.
I'd be more than happy to go through this all with you at some point if you'd like over Skype and take a look at your setup and offer some suggestions, feel free to contact me through nick.wallace@freespacevr.com.au