[verizon]

yes under 100g is low, but not very low. Atkins recommends 20g or less to start with .
You should not have a problem with getting all the glycogen you need - that's the reason fro eating plenty of protein and fat on this diet, to help you convert to using it and so that you never have to use your own muscle protein. So you don't have to worry about 'preventing some protein form being converted', anyway most of your ketones come from fat conversion and this is part of how it works - your brain needs fuel and you have loads of it stored away, but if you keep giving it 'easy' fuel it won't get on and hunt out the fat to convert.
I bet you are getting carb withdrawal because most people do. The symptoms seem classic - feel ill, eat the thing you are addicted to, feel better for a bit, then feel ill again. You just have to go through the bad part - read the posts about 'Atkins 'flu'
Post some of your daily menus, people will help