I have done this before also. I do not remember all the details, but here is roughly what needs to happen.
You need to request that the overage and any associated gains/losses get refunded to you. I think the deadline is 4/15 of next year, but I recommend doing it now or at least before 12/31. I believe the refund check comes directly from the brokerage then. Mine had 10% taken out. They will send you a 1099-R at the end of the year which you will need to report on your regular taxes as income.
In the end, the overage is just treated as regular income. Sure it had 10% taken out immediately, and any difference you owe gets resolved when you file your taxes.