You could try getting a plastic crate? They are a little better at containing the poop. lol And sometimes they feel more secure and less stressed in a more enclosed crate.
Even though he hopped out of your box, you can still try an xpen. They make wire tops for them so it's almost impossible to escape. Then if you have a pen, he can have a small crate to sleep in, and then get a small kitty litter box or puppy pad that he can go on. If he's only 9 weeks then he can't really hold it more than 3 or 4 hours. You'll probably have to deal with the pooping for a while. It may complicate the house training issue slightly by allowing him to go in the house, but it can sure save you a lot of stress and clean up, and save the puppy stress too, if he has a way to eliminate during the day. As he grows up it won't be hard for him to learn that he really needs to go outside all the time now. You can phase out the litterbox. Also you can just leave a litterbox out in the house all the time while he's young. Still take him out lots and encourage the eliminating outside, but then he has a safe haven indoors to if he really has to go! Going on a puppy pad or in a special box that is scented to entice bathroom duties is very different than the dog just eliminating wherever it feels like it in the house.
Also it sounds like you got him aweful young, he really should have stayed with his littermates a couple weeks longer. Yes, dogs poop more when they are stressed. It may take him a few more weeks to settle in with you.
I would try just newspaper in the crate. I know they love to shred it, but it's the safest thing in that case. You don't want them to get a blockage from fibers. Don't feel bad about not putting anything in the crate if you need to. My dogs don't have anything in their crate, they have always been shredders so I just don't do bedding anymore, period. They have free roam of the house and all furniture day and night, except the youngster is crated when we're gone. But they only have to deal with crates when traveling or babies and that is when they are more stressed and likely to shred. I have one I guarantee will go at it the second you close the door. The others can be trusted occasionally depending on the situation. But they are just fine on the crate bottom.
For feeding, you still should be feeding twice a day, he is aweful young. I would just give him a minimal amount in the morning, maybe a handful of kibble. Then you can give him a bigger portion when you get home from work. Then also if you need to add in another evening snack to make sure he gets it all, you can.
Just remember, puppies require a lot of patience! 
Whatever you do, be consistent and it will pay off in the long run.
Also, I live in SE Mich, so if you ever need any help with things, don't hesitate.
