I went through an audit in 2006, the year after my divorce and changing employers... contracting my services out for about 4 months threw a red flag, according to the Wausau office.
I had to take 4 years.. the current and 3 prior years of all tax records with me.. also I had to explain what I expected my income for the next couple years to do for my file.. since I expected a pretty significant drop in wages... settling for work in my area instead of moving for a higher income..
It started out as a phone/mail thing which quickly changed to the Wausau (Rothschild) office...
While it wasn't comfortable explaining your income and why things change... with all the records in order it wasn't a horrible experience, but I can think of a couple thousand things I would rather do. lol.
Biggest thing for me.. being I do my own taxes, is what if I missed a tax law here or there... a little bit of the unknown since you hear these stories of how they can bend you over.
If I were you.. with the amount of question they ask, I would consult a tax expert in your area.. a consultation at the very least to make sure you have your records prepared accordingly before the meeting.. since your employer botched your W-2's.
I would approach your HR department with the issues you face because of their error.. they might help pay for the tax advice.
Good luck.. my experience was truly just an audit of why my incomes changed 3 times in a single year and why they were significantly different... Normal.. Higher than normal then significantly lower than normal.
You sound to have a more complex issue.. hopefully it works out without much pain.
"The oranges are dry; the apples are mealy; and the papayas... I don't know what's going on with the papayas!"