Your results are incredible. I've been wanting to do something very similar here in Yosemite.
How did you manage to capture 42 images without having drastic changes in color & lighting from the beginning to the end? I haven't tried this because I've assumed it's not possible around sunset when the light changes so quickly.
Good question: in the blue-hour image, each exposure was 5 seconds each. For each row, that meant just over a minute passed from the first exposure to the last. I was shooting from left to right. Consequently, the brightness of the right side of the image was greater than the left. From row to row, however, the blending that happens in photoshop during a stitch of this sort did a good job at evening out brightness differences from top to bottom.
All it took to make the left-to-right brightness more natural was a graduated mask across the right half of the image to knock down the exposure just a touch (about 1/3rd of a stop, pretty much).
Oddly enough, I didn't need to do this with the alpenglow image (or didn't feel the need to do this). If you look very carefully, you may be able to see that the light level is just a tad lower on the mountain peaks to the right than they are on the left, but I think, visually, the mind might write this off as being just how the light was striking the mountains. The exposure time for each image in the alpenglow stitch was 1/20th of a second, if I remember correctly, so not as much time between the first and last images of each row.
Also, I've been doing multi-row panoramas for a couple of years now, so I've got the technique down pretty well with my current gear, so I'm able to work pretty quickly when the situation calls for it (changing light conditions, moving clouds, etc.)
