The IRS doesn't file your tax return, but calculates your tax liability based on some information they have - that would not constitute the filing of the tax return.
If you did not file your tax return - you should file it and calculate your tax liability regardless of previous IRS calculations. Most likely - your calculations will provide better tax refund - because the IRS usually do not worry about any deductions or credits.
Regardless of your filing status - you will have one exemption for yourself if nobody could claim you as a dependent.
Additional exemptions should be added for each dependent you claim on your tax return - see for reference form 1040 lines 6 (a)-(d) - http://www.irs.gov/pub/irs-pdf/f1040.pdf
I would suggest to prepare your tax return for each year you did not file the tax return and calculate your tax liability or refund.
You may have a local tax preparer to help you or verify your filing.
There is nothing to dispute unless the IRS would not agree with some numbers on your tax return - so just send them to the IRS and we will hope that everything will be good.
Let me know if you need any help.