Is it too late to withdraw the money now since it is almost 3 months after closing. I want to use the money to apply it toward the principal of the mortgage loan.
You must have a very low mortgage. With proper investment strategy your $10,000 in an IRA should grow much more than the interest you'd save by bringing down principal today. Think about it.
Too late ... you had 120 days before the closing to make that distribution.
The IRS documents I read say within 120 days of closing.
Where does it say the withdrawal must be prior to closing ?
First home. Even if you are under age 59½, you do not have to pay the 10% additional tax on up to $10,000 of distributions you receive to buy, build, or rebuild a first home. To qualify for treatment as a first-time homebuyer distribution, the distribution must meet all the following requirements.
It must be used to pay qualified acquisition costs (defined next) before the close of the 120th day after the day you received it.
It must be used to pay qualified acquisition costs for the main home of a first-time homebuyer (defined below) who is any of the following.
Yourself.
Your spouse.
Your or your spouse's child.
Your or your spouse's grandchild.
Your or your spouse's parent or other ancestor.
When added to all your prior qualified first-time homebuyer distributions, if any, total qualifying distributions cannot be more than $10,000.