My pup - a Bordoodle (Border Collie X Poodle) - will be 12 weeks tomorrow, and I could have written your OP! I created a thread a week or two ago about the biting in particular, and honestly - I did regret him at that moment in time, as I gained yet another scratch/tooth mark/bruise/something drawing blood!, from him.
When he bites/mouths now, we say "too bad" and leave the room for a few seconds - he barks or whines when we go, but when he stops we return. He's learnt quickly - over a couple of days - that biting/mouthing (skin or clothes) results in the loss of the attention, and it seems to have really reduced it. I haven't had a new 'injury' in 3 days now, it's amazing!
We're in a similar situation with toileting - he knows he gets a treat for going outside, we take him regularly, but sometimes it seems he just thinks, 'sod it, I'll wee right here'. We seemed sorted with poo-ing, but over the past week or so he's decided a particular spot in the conservatory is his preferred place for that. We'll continue plugging away at it and he'll get there.
My boy will happily sleep in his crate overnight (albeit with me still sleeping on the sofa - he needs taking out at least once during the night still), but he just will not sleep in there during the day. I'm hoping to work on this over the next couple of weeks so that he can eventually be left for a short time - someone is always about, but it's been really tricky trying to balance things to make it work at times!
I guess this was a long way of saying - like you, I had serious puppy blues, even cried the one night because I had no idea how to deal with what seemed to be incessant biting, but it's starting to improve now and I'm mostly enjoying him again. I'm hopeful that by 16 weeks he'll be much better with the toileting and things will really pick up. I hope it will for you too! :-)