My wife is from the Czech republic. She overstayed her 6 month tourist visa. We are ready to begin immigration proceedings but she has had her purse stolen along with her Czech passport and I-94. I found that we can get the I-94 replaced with the I-102 form but how do we get her passport replaced without going back to Czech?

I would get an immigration lawyer to deal with this. The fact that your wife has overstayed her visa makes her deportable. The passport should be easy to replace, you can probably just take her to the Czech embassy. But, the I-94 is a different story. You should get some one to help you that knows what they are doing (lawyer). I would have done that.