I do it that way so that it is in contact with the wort for longer, a bit like a dry hop. When I say I boil it, that is just bringing it to the boil to kill anything that might be on it.
There's no might about it, they definitely are smart enough. I've had an ongoing war with rodents, rats rather than mice, at my farm for years. I put down spring traps and they work for a while but they soon start avoiding them. I'll switch to poison pellets which takes out some more but these...
The trouble is they are quick to learn that traps kill them and so you'll never get them all. Admittedly they learn about poison too after a while so swapping between methods is actually the best tactic.
Actually I was suggesting you take a look on facebook at the cider making groups to see how others are doing it. It might give you some ideas.
https://www.facebook.com/groups/cider.apples.and.cider.making
https://www.facebook.com/groups/330304940374116...
Many of the orchards in the UK sell their juice directly to cider makers who go and pick it up themselves. I think you'll find some groups on FB that might be worth looking at to get some ideas.
I use a paint stirrer and a cordless drill most of the time. Seems to do the job.
I've heard there's a possibility of over oxygenating the wort using pure O2, though how true that is I've no idea.
The dark colour could indicate your suffering from oxidation. A 25 gallon container is far too big for 5 gallons. Also you shouldn't be opening it until you're ready to bottle, especially with that massive head space.
I might be wrong, but it looks to me to be a case of demonic possession. Have you or anyone in your household been practicing any of the dark arts close to the fermenter at all?
I had this myself once and ended up having to get a priest in to bless the place, as everything I tried didn't seem to...