We will try to make him sort of a crate out of baby gates from baby's bed, more to give him his private space but also to create the time for our toddler to play freely without our dog (all the toys end up being chewed up).
We feed him 3 times a day.. after his morning walk, after his midday walk (short) and after his big afternoon walk (around 4-5).
We feed him Canidae's ALS and we feed him little less than 1 1/2 cups.
And the questions

1. We (still) have a problem with peeing and pooping indoors.

He still has accidents with peeing.. less than before but I expected he'll be trained by now. We made him a spot in the hall where he can pee in the wee hours (during the night or in the early morning, before I get dressed for a walk).. our neighbors are my parents so they don't mind him peeing there but I expected he won't b needed it, he'll manage to wait until we go outside. Maybe I'm impatient and maybe I don't recall how long did it take for Ginger (the dog we had before him) to learn to wait until we're out of the building.
Also, he doesn't have clear clues that he has to go – only I'm able to understand that he needs to go. And, when I'm at home he usually doesn't have any accidents but with my DH or when DD is alone.. accidents happen.
Sometimes he has to poop in the middle of the night. If I don't hear him and let him out of the apartment, he poops and then tries to clean the whole thing by eating the poop (yuck!).
He goes for a walk in the evening, about 3 hours after his last meal and if he doesn't poop then, my DH walks him shortly before bedtime just to give him the chance to poop outside the house. And he still poops inside sometimes.
He is on a schedule, has at least 3 walks daily – first thing in the morning, an hour before bed time in the evening, and one big walk in the afternoon when he can run free without the leash, and if we can squeeze in, 2 10-minute walks (just to take him out to pee and poop on the grass).. beside that, I take him out in the hall after the play, after his naps, after his meals and whenever he acts suspicious.
2. His stools are still not firm all the time (at least one stool a day) and smell horrible.
We feed him the least amount of food recommended for his weight. Beside that, he gets raw carrot or apple from time to time or a dog biscuit or treat of some kind. I can feel his ribs easily, he really is skinny. He eats Canidae ALS and likes it. I tried raw but he doesn't want to get anywhere near it (I tried different types of meat).
3. I fear he is hungry. He is constantly asking for food, jumping around the table when we eat (I'm working on that.. he acted ok when he was younger but now it's a mess.. he's trying to steal the food and if I use the leash he barks and yells and chews the leash) and trying to steal the food.
He once jumped at the table and ate DD's soup (that was the first and last time we left the food unattened on the table). And he'd eat anything he'd find while walking.. everything has to end up in his mouth (not only other dog's poop).
Is that normal behavior or he really is undernourished or we need to switch to another type of food? I wanted to increase the amount of food he gets but didn't know if that was a good idea because of his stools.
That all for now.
Thank you all so much for your suggestions and help.