You make a mistake in assuming that in order for something to be divine it must be completely original.
To understand the Torah and G-d's intentions and its applicability to modern times does not require cutting off and ignoring the societal backdrop of the Torah's historical time period. This means that although there may be some slight similarities in certain laws to the Code Of Hammurabi or similar themes in the flood story to the Epic of Gilgamesh, its not concerning. The Torah does not claim to be the sole source and originator of judicial law, society's were governed by law, way before the Torah was given i.e. Derech Eretz.
Rather, the Torah is coming "to set the record straight". Meaning that the intention of "re-stating" the laws either to infuse mundane societal laws with divinity and the novel concept of a G-d centered moral code which up until then was primarily dictated by rulers.
Regarding the flood story, the Torah repeats it in order actually tell the "true story" of the flood, devoid of all the idolatrous aspects that crept in over the generation as a result of it being retold again and again.
Furthermore, without an intimate knowledge of Akkadian or Hyroglyphics or other ancient Semitic language its almost impossible to claim that verses were taken from one source to the other. The nuances of these languages can sometimes change the entire meaning of a inscription. (Heard from Rav Aharon Lopiansky)
In regards to similarities to the building of the Mishkan. Human history is rife with mans desire to reach out to G-d in many forms of altars and worship centers. But the difference in Judaism is that the commandment to build the Miskhan: "ועשו לי מקדש ושכנתי בתוכם": marks the first time that G-d reached out to man to build. That alone suffuses the keilim - holy vessels in the Mishkan with profound divinity.
Thus, you could find similar, or even the exact same floor plans of the Mishkan anywhere in the world, but at its core and essence it is completely different entity from the Mishkan. (Heard from Rav Yechiel Perr, in writing here as well)
I suggest the Shiurim of Rav Ahron Lopiansky on the topic archaeological evidence and the Torah which can be found here.