Thanks for the response, one thing I'm learning to love about your product is how attentive and helpful you are!
So, the problem ditching the 1st and 3rd shots and going with the middle image (an option I was going to pursue originally) is that I lose key frames. The hyperlapse moves too fast as I took the 3 bracketed shots and then moved 3 paces forward. Having those 3 frames for every "position" really helps this feel more fluid and less jerky. Plus I really like the motion trails of the people as they walk by.
I use Photomatix Pro 5 (
http://www.hdrsoft.com/) to batch merge multiple bracketed images into HDR images. Because my shutter speed went from 1/4 sec up to 1 sec, the amount of movement between shots causes extreme artifacts/ghosting in the images.
So, is there any way to "bake-in" the new exposure settings I made when I used Match-Total-Exposures? I could always export to JPEGS first and then use the basic workflow, although I'd lose out on all the other control I'd like to have like finessing the RAW camera settings.
I've certainly learned a lesson to not cause these issues for myself in the future by not shooting bracketed exposures if they won't work in HDR.