In this case, the most straightforward approach is to amend your previously filed MFS return as you indicated. Via amendment, you can change filing status from MFS to MFJ. On the amendment, you would add all of his income items, leading to a complete return that has income from both spouses fully reported on one return.
Estimated/extension payments are associated with social security numbers. When preparing the amendment, you want to make sure to indicate that the extension payment was made. The IRS will reconcile this against the primary and spouse social security numbers on the return. In some instances, the IRS may not recognize the payment if it wasn't associated with the primary taxpayer on the return. In this case, they will send a notice, and you will need to respond to the IRS accordingly with proof of the payment.
Note, on an amendment, you cannot amend from MFJ to MFS, so if you proceed in this manner, it is not reversible.
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