Where does the Gra mention the idea that Sefer Devarim is split up into parshiot representing the centuries going into the 6000 millennium? There is another idea that Ki Tavo fits into the years of the holocaust,where is this idea from?
The first idea was stated in the name of the Gra by R' Hayyim of Volozhin, who mentioned it to Rav Yitzhak Margoliot, who mentioned it to R' Shmuel ben Avraham of Slutzk, who published it in a collection of sayings of the Gra (Koenigsburg, 1864). My source for that is HaMeor HaGadol (המאור הגדול: הגאון החסיד מווילנא זללה"ה), published in two volumes by יששכר דוב קרויזר (Makhon Moreshet haGra: Jerusalem, 2004).
In volume 1, the second comment appended to Deuteronomy 25:15 reads as follows (this is a direct quote from R' Shmuel ben Avraham's sefer):
I do not know to which events R' Shmuel ben Avraham is alluding, since for them to take place within the seventh century and to precede the publication of his text they would need to transpire between 1840 and 1864. It may have been the second of the Odessa pogroms in 1859 that he had in mind. In any case, if we were to utilise the same schema, only the first six years of the Shoah (1933-1939, or 5693-5699) would correspond to Ki Tavo. The events of 1940-1945 (5670-5675) would correspond to Parshat Nitzavim/Vayyelekh instead.
Speaking for myself, I have not heard this particular idea before anyway, and I wonder if it might be possible that you are confusing Parshat Ki Tavo with Parshat Bechukotai? If so, the source for your idea may be what R' Meir Simcha of Dvinsk says in Meshekh Chokhma, on Leviticus 26:44. It's too lengthy to quote in full, but he speaks of the nature of the exile as being one in which people become accustomed to where they are, as a result of which God causes a great storm to come and violently uproot them, reminding them all that they are Jews.
A little way into this discussion, he relates these warnings specifically to those Jews who desist from learning their laws, who learn languages not their own, who engage in ways of destruction and not in ways of reparation, and who consider Berlin to be Jerusalem (יחשוב כי ברלין היא ירושלים). He then promises another storm of terrible proportions, which you can read inside for yourself.