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Can you provide some details such as - how many quarters, which quarters, what is the total dollar amount (approx) of tax invlolved by quarter, what is the approx total dollar amount of penalties, how much do you still owe, etc.
The more information provided, the more likely we can construct a response that might help.
Bearing in mind that the IRS is not required to reduce or remove penalties - your best bet is to write a detailed letter emphasizing that 1. you have corrected the situation that was leading to the penalties, 2. you are current with respect to all tax filings and tax payments since Q1 2009, 3. the payment of additional penalties presents a financial hardship for the business, and 4. request abatement based on the above.
You should keep the letter on point to the circumstances and request - you are trying to convince the IRS that enforcing collection of the additional penalty amount would not serve any purpose as a deterrent because you have already addressed the situation and are taking the steps necessary to ensure that it does not happen again AND that enforcing collection will harm the ability of the business to continue to operate profitably. In this regard, the circumstances that led to the original delinquency usually should not be discussed - they have heard all the reasons before.