Wow, thats a pretty well shot section of the film. Takes me home to the lest 6 years of my life. The first 15 seconds are them driving up US 89 north of Flagstaff and the Little Colorado River, through the Painted Desert Bad Lands out there. At 16 seconds they start up US 160, down by Tuba City's airstrip as they start the grade up to the table below Tuba City. From 51 to 55 seconds, as Peter points north, they go around the bend on 160 that turns the road more or less east, and you can see O'Leary Peak and the main body of the San Francisco Peaks north of Flagstaff. Then, around 1:00 to 1:07, they look down on the area where Tuba's airstrip is, but does not appear to have yet been, in 1968 or 1969 (and that wasn't shot in March for Spring Break, it looks more like May to June).
The next 9 seconds of sunset appear to be over Skeleton Mesa, but it's hard to really know. It is not Black Mesa. However, if my assumption is correct that those sections are of Skeleton Mesa, then it is more likely June, as the sun is very far north for the sunset and it couldn't be March for Spring Break. The Junipers on some small flat hills are part of the lowest sections of Black mesa north of 160, and out 2/3 of the way to the Yazzie Tire repair place, 7 miles or so west of Kayenta. I think the next 4 seconds is a section of rounded rock out cropping on the side of 163 just north of Laguna Creek, and it would be part of the Comb Monocline/ Ridge. At 1:19 you see Owl Rock, north of Kayenta, and at 1:21 it's Agatha, on the opposite side of US 163. 1:24 looks back on both feature which straddle 163. The next few seconds has them pan over Monument Valley. I think they are then out of order looking back on a mesa north of Kayenta, out near a turn off for a family I knew and their farm that was up a canyon. Some untouched ruins out there with 800 year old corn, and grain storing huts(?) stinking of rodent urine. 1:47 pans across the Abajo Mountains, and the sun sets on monuments in Monument Vally, sort of off route and south of 163.
Interestingly, it took them way too long to travel from west of Tuba to Kayenta, but they got to Monument Valley way too fast. Maybe they stopped for some Navajo Tacos in Red Lake?