Hi koe2moe, I am rushing off to bed now so will only reply quickly, but sorry you have had such a hard time and sorry your DS has been so poorly (and you so poorly too!).
One thing from the start is that if you and your DH and DS are happy co-sleeping, you don't HAVE to change it. There are always ways to encourage DS back into his cot at whatever age and time you think is right.
I would, though, ditch the middle of the night bottles. He doesn't need them and it isn't going to help with his eating during the day. I have found that when my DS is ill he just isn't hungry generally, so offering water overnight is probably enough until he is feeling better.
The bedtime bottle I don't think is a problem for a while longer! I hope not anyway because I still do it (well, bedtime BF but same thing). I can't really see the rotting teeth being a problem from just having a bottle at bedtime because it's not like even if you tried to brush his teeth after the bottle that you would really actually get to clean anything (my DS just eats the toothpaste straight off and asks for more!). I think the main problem for rotting teeth is letting them sleep with a bottle of milk or juice because they might fall asleep sucking constantly with the liquid just sitting on there.
You have a lot to deal with right now. If it were me, I would probably try to tackle getting him to nap in his cot so that you can have a break in the day. And tackle no more bottles in the middle of the night by doing gradual withdrawal or WIWO. And maybe try to settle him in his cot at bedtime, after his bedtime bottle. Then if you want to co-sleep from when he first wakes in the night, or whatever, in order to get all of you the most rest possible, then you could do something like that.
Hope he is feeling a bit better soon.