How do I provide documents to the IRS that I do not have any more?

It sounds like your tax returns are being audited by IRS. You are required by law to maintain tax records. If you are not able to substantiate the numbers you claimed on your tax returns with the relevant records, IRS has the authority to make the changes they deem to be necessary and you will be assessed additional tax, interest and penalties.

There is very little excuse for not having documents that relate to your 2008 and 2009 returns. You indicate "I...do not know why they are bothering with me...." The IRS can audit anyone. The IRS is authorized to ask for paperwork that is necessary to help it understand your tax obligations. The fact that you "do not have all the paper work they are asking for and do not want to be hit with all kinds of charges" is not the IRS's problem - that is your problem. The fact that you "have not done anything to hide money or been misleading" is, of course, very important. Now your task is to make the IRS comfortable with the fact that you have properly reported all of your income and properly taken all the deductions. How will you do that? I cannot help answer that because I do not have your facts. However, if you have been honest then there should be a way to convey the information to the IRS to make it feel comfortable. Without knowing the facts I cannot even begin to guess how to accomplish that.