You need to pay the $2000 by 04/18 if that is your net tax bill for 2021. And you can pay directly through the IRS site. You should pay the amount due after taking into account the amendment.
You have already filed, so you are not going to be hit with a late filing penalty. The only thing you can get hit with is an underpayment penalty. Underpayment penalties are assessed if you don't withhold or pay enough tax on income received during each quarter.
If you pay the $5k, you will get a $3k refund later. But you can just pay the correct amount and not have to wait on the IRS.
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