Short answer: Yes.

Father-daughter incest: The Amarna Letters (EA10, 11) show that Pharaoh Akhenaten married his daughters Meritaten and Ankhesenpaaten. This is corroborated by Letter EA155. Other pharaohs who are thought to have married their daughters: Tao II, Ahmose I, Amenhotep I and II, and all 4 Thutmoses.

Father-daughter incest nevertheless rare compared to brother-sister incest. During the last Egyptian dynasty, the Ptolemies (from whom Cleopatra sprung), there seems to have been only brother-sister incest for 275 years. As for mother-son incest, it seems to have been nonexistent. John Richardson calls mother-son incest 'totally alien' to Ancient Egyptian culture.

Note that incest may not necessarily have been sexual in nature. For example, Janssen explains incest in an Egyptian context as more of a political arrangement, where the daughters might only have had to perform ceremonial wifely duties. Yet it is undeniable that such arrangements did sometimes result in sex and even offspring. Senofru, a Fourth Dynasty Pharaoh, married his daughter Nefretkau and produced a son, Nefermaat.

would normal citizens or lesser nobility be able to have this sort of arrangement? Or is it strictly limited to the royal family?

L Manniche in the 'Sexual Life of Ancient Egypt' answers your question well.

Basically, there was a divide in attitudes towards incest over the thousands of years of Egyptian culture. In the last 3 centuries BC (Ptolemies), incest was so common that Egyptian lovers used 'sister' and 'brother' as terms of endearment.

But in pharaonic Egypt, incest was the exception, not the rule. It seems that registered cases of incestuous marriage were only found among the royal family. Among ordinary people, 'there is only one [instance] that can be said to be incestuous; two are 'almost certain', two more are 'unlikely, but possible'. Manniche concludes:

Nothing suggests that incest was common among ordinary people in Ancient Egypt.

Follow up question: would normal citizens or lesser nobility be able to have this sort of arrangement? Or is it strictly limited to the royal family?

This is certainly not an all-encompassing answer, but I know there is some debate as to whether Akhenaten took his daughter Meritaten as one of his wives. It seems it may just be slander based on his stance as "the heretic king," but we should examine the accusation. She was named Great Royal Wife, however this was a ceremonial position moreso than an indication that she was a sexual consort. She was recorded as having a husband who was not her father. So it seems, as far as I can tell, she was symbolically his wife, not his wife in practice, though we just can't know for sure.

I'd like to see more answers to this to address whether this would have been considered taboo. I always got the impression that even this appearance of parent/child pairing was considered taboo.

Follow-up: do we have any knowledge of genetic diseases in the Egyptian royal lines, like we do with the Hapsburgs?