IRS struggles

I got a letter in May from the IRS. Yeah, one of THOSE letters. It was a letter telling me that the IRS didn't agree with my tax filing for 2012, and explaining that they took the liberty of doing my taxes for me. Then it said that, by their calculations, I owed them another $8,400 and change in taxes. I had two options: I could either send a check, or I could send a letter as to why I didn't agree.

They disagreed with my income, because they claim that I didn't report income from a 1099 that I had received from a customer that I had done some consulting for. I checked, and the income HAD been reported, but on the form for reporting business income, and not personal income. I sent proof.

They disagreed with my reporting of income from investments. I under reported my investment income by $4. I couldn't argue there. I forgot to include the $4 in interest that I had earned on a small savings account.
 
They disagreed with my deductions, claiming that I had taken a lifetime learning credit for a school that is not confirming that I was a student there. I have receipts and a 1098-T. I sent them in.

I just got a follow up letter. They agreed with me on the reporting of my income. Now, according to the IRS, I "only" owe them $1,200. They still say that they school is refusing to verify that I was a student there. I have a 1098-T. I have bank records, a $12,000 student loan, my student ID card, and receipts to prove that I was. If I have to pay taxes on this because I can't prove I attended this school, then why should I have to repay the $12,000 student loan. After all, if I wasn't a student of their school, then how did they give me a $12,000 student loan?

So I will be sending the next letter out this weekend.