@Newerth
All new software comes with a bit of a learning curve 
Here’s the fast/quick and in-a-nutshell way to use Hugin to stack bracketed images:
You see me changing the Anchor position (A) in the Photo tab, this is the image Hugin will align all other images from, I always use the middle one.
The Anchor exposure (C) should be set on the image that has, on average the best exposure. In general that would be the one in the middle, but it seems that in this case it is the first one. So I did not change that one.
The rest of the actions you can just copy the way I did them when stacking bracketed images. Only one that you might want to change is the Hugin’s CPFind setting. This takes moving clouds into account.
You can do a whole lot more with Hugin, fine-tune things, use the masks tab to remove/include portions add/remove control points set processing options etc etc And that’s just the stacking side of Hugin (it is a panorama stitcher at its core…).
The Hugin manual explains all the options in detail and there are some tutorials to be found on-line as well. Just experiment a bit to find out if this is a solution that you can work with.
An alternative (with a warning…):
If you are comfortable with using the command line you could use enfuse, which is part of Hugin, to get a good starting point. This, again, use non-RAWs as input.
Something simple like this should do the trick:
enfuse --exposure-weight=1 --saturation-weight=0 --contrast-weight=0 --entropy-weight=0 *.tif
Or a bit more readable:
enfuse \
--exposure-weight=1 \
--saturation-weight=0 \
--contrast-weight=0 \
--entropy-weight=0 \
*.tif
Here’s the man page: man enfuse(1). Some of the options are explained and you might want to add some (not really needed in most cases).
The warning I was talking about is about this: This will not align the images first! You need to be/make sure that they are aligned to begin with.
@gaaned92
That might partially be the input files, they could have been better, but they should do.
