What type of food are you feeding?
It may be a food with too much fiber in it. A lot of grocery brand foods have too much fiber in it which will cause your puppy to poop. Also, some of those super duper holistic/organic types of foods will cause puppies to poop a lot due to the fiber in it.
Having GI parasites isn't going to help much any. Maybe after she is done with her medications it will help her not have to poop so much.
I understand your frustration and lack of sleep, but every 2 hours is pretty normal for a small breed puppy.
Is her crate small enough? Sometimes when we buy the adult sized crate for a puppy its counter productive. If the puppy is able to poop or pee in its crate and sleep somewhere else, than its too big. You would want to put her in the smallest crate possible. A 10 week old boston is pretty small, maybe borrow a cat crate from a friend for a while until this is under control.
As for the poop eating, since this is just adding to the problem... purchase For-bid. FOR-BID Stool-eating preventative (12 packets)
It will help her to stop eating her poop.
Eating poop is a natural thing. There are many dog people and websites and theorys why dogs eat their poop. Truth be told, it is just a natural thing that they do. Its disgusting to us, and every dog will do it. But seeing as how your pup is pooping in the crate and than eating it tells me she is wanting to stay clean. That is a good thing :) Also, before starting the For-bid.. give her a good bath and clean that crate out with an enzyme-based cleaner designed for pet odors. Take the smell completely away. That should help.
Throughout the day, put her in her crate and start training her to old her potty. House training is more than just a mental training, it also a physical training. So start during the day... keep her in her crate for 15-20 minutes, than go outside. Give her the command to go potty. Don't play with her, don't interact with her.. just stand there and repeat "go potty". Once she potties.. give her lots of attention and than go back inside. Do that for a couple of days, increasing the time she is in the crate. And I would do this a few times a day, especially after eating!
Also.. 3 times a day is too much. Puppies only need to eat twice a day. If you are feeding a balanced diet, than the pup won't feel hungry in the middle of the day. The more food you feed her, the more she is going to have to poop. Follow the recommendations on the back of the bag and base the amount on her energy levels. If she is calm, than give her the lesser amount. If she is wild and crazy, give her the higher amount and split it in half.. Half in the morning and half at night. See if that doesn't help you. And during this time, I would also suggest to not feed treats. Get her use to your routine. Treats will just add to your problem at this point. If you feel the need to give her treats, than get a soft, chewy treat that you can break up into pieces. So you would be giving her one treat a day, even though it would be broken up into pieces and given throughout the day.