Haraputta,
First off, I would appreciate you for not sending any PM to me anymore because I normally don't read each of them. You might think that I'm purposely not answering but the truth is I might not be reading them even if I might open them. And it's not that I totally don't respond to PMs that I receive, rather I just don't read them most of time to answer to them.
Secondly, I suggest you not to open all kind of threads for the same questions. Try to ask the questions on one thread so that people could get the whole picture of your situation at one place than going to all over the board.
As for your specific situation then it's true that aiding and abetting (harboring) an illegal is a federal crime but I've NEVER heard of this law of being ever applied or sought out in any case even though I've been on this site and other more for many years and also dealt with thousands of cases similar to yours...This law is more of being just on the book than being ever used. Not always all laws are implemented, for example, USCIS can detain and deport anyone who is illegal here, which includes spouses of US citizens who have pending application for adjustment of status. Some might think (obviously mistakenly) that INS cannot detain an illegal spouse of a US citizen who has a pending AOS... but anyone who thinks so is wrong. Why? Because immigration laws very clearly state that INS should and must detain anyone who is illegal in this country.
Laws don't waive illegal-spouses of US citizens from detaining and deporting if they are caught. Illegal spouses are just allowed to file paper here in the United States to adjust their status if they are the beneficiary on a visa petition filed by their US citizen who is an immediate family, but that doesn't mean INS cannot detain these illegal-spouses of US citizens. It's just that INS has chosen as a matter of their policy (not as a law) based upon their own discretion not to detain those people who have pending AOS, but that doesn't mean they cannot detain an illegal (regardless of who that illegal is). That's why it's important not to come in contact with law enforcement agency (for doing a crime or anything for that matter) and with INS (not administrative branch though) if someone is illegal; otherwise an illegal would be detain even if s/he is the spouse of a US citizen and has a pending AOS. Having said that, I just want to say that not always all laws on books are implemented.
You have nothing to worry about in your case. Your wife's illegal status won't be an issue at all. The information on N-400 about spouse and the legal status of spouse is NOT asked to find out if applicant is harboring any illegal or not, nor it's asked to know the legal status of the spouse to take any action. Instead, this information is asked primarily to keep marital information on the applicant and to know who was/is the spouse of the applicant so that some lies/frauds could be traced out in accordance with other govt. records to determine moral character of the applicant.
Believe me, officer wouldn't even ask you anything about your wife's status at all. I've NEVER heard/seen any case wherein applicants were specifically grilled/asked on why s/he is harboring an illegal or anything like that. Also, there is no any question on N-400 which specifically asks if applicant is harboring any illegal; rather it's asked if applicant has helped anyone to gain entry into the US illegally, which is different than harboring an illegal. Just don't worry about this issue. And don't believe everything what you hear.
As for the taxes, then it is a big problem if you filed your tax returns (for whatever year) as a single status if you were actually married. This a ground to deny the citizenship, and INS do check this kind of inconsistence to fret out the fraud/lie. You better file an amendment to your those tax returns which are inaccurate. IRS won't ask anything. And ITIN number can be used for your wife if she doesn't have a SSN. IRS will issue her ITIN number if she doesn't have that number yet. If you don't correct your tax returns, you will risk your citizenship application to be denied or be revoked in the future. Don't take that chance. But I can guarantee you that the illegal status of your wife won't be an issue at all.
Good luck...