If the return you are preparing is the final return and you made a distribution, then any gain or loss from the sale of the shares would be passed through to the beneficiary on a K-1 (along with any income - dividends - that might have been earned).
You need to adjust your tax year, If you select a fiscal year for the estate, that year could begin in the tax year the estate had income and was, therefore, required to file a 1041.
The fact that the named beneficiary was not on the account that held the stocks, is irrelevant; that is still the beneficiary according to the will.
