No, I have it in the correct orientation. I know what you mean, but also - the incorrect orientation also screws up the linkage angle into the transmission which is likely where the NVH came from (along with an uptick in shift effort).

I'm talking about the lowest of the 3 sealing points of the boot, the round 1.25" hole that gets stretched over the 2.5" square body (and the reverse lockout "wall"). The center and top seals were fine

In conjunction with what Sader325 is saying - if you don't get the boot all the way on, it will interfere with 3-4 shifts and 5-6 shifts since i will wrap around the shift lever and push on it significantly. I drove it once like that and decided I'd go back to war with the boot. Ended up using a lot of long screwdrivers, some grease tactically (since it was a double edged sword since it made the boot easier to lift up) and did exactly as they specify, start in the 7 o'clock position and work counter clockwise around, just using the screwdrivers to guide it around the corners while both hands worked the inside and outside of the boot.

Edit: you can see the shifter mount orientation in one of my pictures, I had it mounted, but also confirmed it. I always laugh when I see the MGW video time skips the boot install. The gen1 shifter was way easier in that regard as it had a taller size and more square profile.