They aren't going to be "full" per se. You can just feel that they aren't empty. It's hard to explain, lol. If you bottle feed a baby they get a "full" tummy. When babies are on momma, they just take little slurps here and there at first. So, they are never going to really be full. If mom has milk, and they babies aren't getting weak, then they are more than likely getting milk. Especially if they don't care about milk coming from a bottle. Try the whole milk (make sure you warm it up) and if the baby doesn't really care about that either, I would guess they are probably getting enough to eat. 
 
Don't worry about undoing the bonding, you didn't. A little bit apart isn't going to undo things. That being said, the first few days, momma doesn't really leave her kids to do much but eat, so don't worry about momma. 
Some people have varying opinioins, but in my opinion, if you keep things super clean all the time, babies can't develope the immune system they need. So, don't worry so much about that. 
 
 
Are the kids acting strong? Up standing good? Walking around, thinking about starting to hop a bit? You say the buckling cries all the time, and that concerns me a bit. Usually they only cry a lot if they are hungry or in pain. 
 
Back to the bellies... do they still look sunken in? They aren't going to feel firm really, just not sunken in and empty. You might try uploading a pic, see if I can help you more. This is something that's just hard to explain, lol. 
 
Also, are you giving mom grain? If not you probably need to be.