The question often asked: Were there seven of each clean beast, or two?

The answer is, seven. The phrase "two by two" in Genesis 7:9 simply means the animals entered the ark in pairs. So the beasts with 7 representatives came in as 3 pairs and 1 oddball each, paired off male and female and one spare wheel. (Note the difference in phraseology: "by two" and "two and two".)

Objection: Genesis 6:19-22 commands two of every kind into the ark.

According to the KJV italics and an interlinear Bible, the word "kind" ("sort" in the KJV) is not found in the original Hebrew text. In other words, it actually says, "And of every living thing of all flesh, two of every shalt thou bring into the ark, to keep alive with thee; they shall be male and female. Of fowls after their kind, and of cattle after their kind, of every creeping thing of the earth after his kind, two of every shall come unto thee, to keep them alive." Wenham's Genesis commentary reads it, "pairs of every", i.e., as a case of mode, not number, just like we do in 7:8-9. In other words, the references to "twos" refer to mode by pair, not total number.

Then what about Genesis 7:1-5 taking seven pairs?

"Pairs" isn't in the original text here, either. The Hebrew actually says "seven sevens". According to H.C. Leupold, "The Hebrew expression 'take seven seven' means 'seven each'", and suggested that the extra one was for sacrifice. Jamieson, Fausset and Brown commented:
> 'This was the general rule of admission, only with regard to those animals which are styled "clean," three pairs were to be taken... But what was the use of the seventh? It was manifestly reserved for sacrifice; and so that both during Noah's residence in the ark, and after his return to dry land, provision was made for celebrating the rites of worship according to the religion of fallen man.'

If Noah did all that God commanded him, which was to bring two pairs of "all flesh" onto the ark, how could Yahweh then command Noah to make a distinction between the number of clean and unclean animals taken aboard and to take aboard seven pairs of birds?

The latter command is an intentional repetition made to fit it all together into a chiastic pattern.