My biggest questions is about separation anxiety(?). Calvin (the puppy) seems completely uninterested in toys.
Totally normal at that age. Hans was not interested in a ball until a couple of weeks later. He did like very fuzzy toys with squeakers, but was not crazy for them for a while.
When not kenneled, he constantly follows me around the house and just wants to sit at my feet or paw at me/nip for attention.
Of course he does. He is a puppy, he has been removed form everything familiar, and you seem to be a cool person who feeds and takes care of him.
Get used to the following, and enjoy it. GSDs are herding dogs and want to be with you at all times.
We go out for potty time, he just sits at my feet unless I walk around the yard.
Take him out on a leash and harness. When he pees, say "pee." When he poops, say "poop." He will soon learn, and it will be very convenient because he will do his business on command. Praise lavishly.
If I put him in the kennel, he cries constantly. I can't figure out if he just misses me or is bored and needs play time. But when I get him out to play, he ignores all the toys. He is making it very difficult to positively reinforce being quiet in his kennel when I can't find 15 seconds of him being quiet to go into the bedroom and praise/reward. On the rare occasions he is quiet for a minute, I go in, click, treat, praise etc two or three times. The moment I leave all **** breaks loose and he makes the most pathetic howling I've ever heard. Is this normal behavior that will go away in a couple weeks or should I be doing something different?
Schedule nap times. Stick to them. Leave him in there and ignore the howling.
The other is food/water. I am taking this week off work to stay at home with the puppy to get him used to life here. We are doing three feedings (morning, noon, and night). Do I give him water all day or only when feeding him? The other is he will only eat out of my hand or off the floor. He sticks his nose in his food dish then immediately walks away. The water dish is of equal depth and he drinks from it with no problem.
Water all day, yes. Remove water access at 7 PM.
Hans didn't like dishes at first, either. It is not natural for dogs to eat from a dish. Puppy will get used to it. But for now, hand feeding is a fantastic way of bonding with him. Teach him to sit and give him food for that.
Walk a few steps, then have him sit and give him some more. Take this opportunity to train and establish trust.
We've only had one accident in the house so far and I caught him in the act. Gave a loud clap/no and carried him outside. Waited for ten minutes and nothing else happened so we went back inside. The issue is we had just come inside from potty time when the accident happened. He had gone pee, but obviously didn't get everything out. Is this just the sort of thing that is going to happen, or is there a way to make sure he gets everything out when outside?
Stay out longer. Take him out on a leash. Watch him like a hawk. Take him out every hour or so, and after sleeping, eating, and playing.
I'm sure I'll have more questions later, this is just what I've got for the first 24 hours...Going to go make some coffee....
Enjoy your coffee and puppy, and welcome to the forum!