Executor, late gift tax return

I've become executor for my mother's estate. Her final income tax return and estate income tax return don't seem complicated, and her total estate is well below the $1,500,000 threshold for filing the Form 706 Estate Tax Return. But she made a cash gift in 2003 that was greater than the annual exclusion amount and did not file a Form 709 Gift Tax Return. The amount of the excess would make little difference in her maximum unified credit. If it had been filed, there shouldn't have been any tax due either at that time or now. How should I handle this? It appears that Form 8892, Application for Extension of Time to File doesn't apply beyond six months after the return should have been filed. It seems that I should file a Form 709 with an attached explanation. Is that correct, and should filing the late Form 709 have any effect on when I should file either of the regular income tax returns? I suppose there would be no penalty based on any unpaid amount due if there wouldn't have been any amount due. But is it likely there would be any penalty based on the 709 not having been filed in the first place?