don't worry
I think everybody else said the same thing....but just wanted to clarify your doubts regarding this. As long as you're waiting to adjust (I-485) your status, your status is very much valid in USA. You or your wife can legally stay here. For work, you need to have either EAD or H1, whichever is available. Your I-94 can be expired, but you can legally stay here as long as you are waiting to adjust. But, EAD/H1 is required to work.
BTW, i did special registration back in March when i was waiting to adjust my status. However, i had EAD. There was no problem what so ever during the registration. If someone has been deported, it must have been for a reason, not because he was waiting to adjust his status. Last week, i got my approval, and got my passport stamped today. Luckily, i don't have to do the registration afterwards.
Hopefully, this helps.