I got caught near the end when the entire composition area of two shots (upper and lower) was the dark tree and the auto exposure compensated for that and over-exposed those two frames (relative to the rest of the shots) by about three or four stops. Next time I try this I'll be aware of the problem and for those two shots at least go to a manual exposure over-ride.
You might want to just lock the exposure for all shots, so that the blending software doesn't have to make extreme corrections for the exposure differences.
The most successful example of this kind of photography I've seen is where you do fixed, bracketed exposres for each position, then do HDR processing on the brackets, so that what you get is essentially three full panoramas at each exposure level, and the result is a full size HDR panorama. Not sure if you do the image blending first, or the HDR processing first.
An acquaintance once showed me his college project, which was to do that entire process described above, but do it four times, making four complete separate HDR panoramas, one each for a different time of day: Night, Sunset, Day, Sunrise. It was amazing work.
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