You are still using an extremely short exposure time. Move that up to at least a couple of milliseconds until we get this figured out. You will need to drop your gain accordingly to keep the image brightness from clipping. Always keep your histogram up (though you can shrink its height considerably from the default).
Otherwise, everything looks pretty much OK in the camera settings.
To export a single frame (or multiple frames) from AutoStakkert, use the Export Frame(s) control at the top right of the image window. Click Current and the program will bring up a normal Save As dialog. Save the image as a JPEG or PNG for posting here. To get the full raw image, use FIT. For a screen capture, look for a PrtScn or similarly named key on your keyboard. If you have a laptop, you may need to use the Fn key. Create a new canvas in Photoshop or whatever image editing program you are using, then paste the image onto the canvas. In Photoshop, you will have to flatten the layers before saving to a JPEG. If you have a Mac, use Command+Shift+4. You then use your cursor to drag a selection rectangle over the area that you want. When you finish the selection, a copy of the area that you selected is saved to the desktop in .PNG format.
I can't help much with the flat, though it is sometimes possible to use a heavily median filtered version of the image as a flat. Regarding the actions that Autostakkert has taken in your "mottled bits", I think that most of what it is doing can be explained by looking at what the Min Brightness setting does.
When you click on the Place AP Grid button, the program looks to see what the Min Brightness setting is, and it won't place any APs anywhere in the image where the brightness is less than that. In my example here, Min Brightness has been set to 35. The disk is fully covered, but certainly there is something interesting going on at the limb and that, being the most interesting feature, is not being represented well with APs, see inset.
If the Min Brightness setting is reduced to 15 in an attempt to force more APs along the limb, the result is this:
Now there are a bunch of APs out in blank space, which isn't going to be helpful at all to the stacking process and can only slow things down, at best. Changing the display brightness also has a major effect on how AutoStakkert sets APs. Here the display brightness has been set to 2 and Min Brightness is back at 35. AutoStakkert tells us that changing the display brightness does not affect the data, which it doesn't, but it definitely affects how the APs are set. AutoStakkert apparently will not use a clipped brightness for the location of an AP, so now there are no APs at all on the disk and everything is out in space.
I don't know what your flat looks like, but I'm hoping that this explains at least some of what is going on with the APs being placed over your mottled areas.
Just to continue one bit further... Clearly, when I do want to tell AutoStakkert to be mindful of detail in the proms and the disk at the same time, AutoStakkert has a difficult time. I handle the situation by letting AutoStakkert do all of the APs on the disk automatically. I like using the Multi-Scale option that has been added in Version 3.1. After the automatic picks are done, I set the display brightness to whatever allows me to see the proms clearly. I clear the Draw APs checkbox, which clears the clutter of the existing APs so I can see what I'm doing. Usually I set the AP size lower by one or two steps, depending on the image. Then I go around the image, manually adding APs anywhere that I think they will help. Simply left click to place a new AP. Right click on APs to delete them (you may have to turn them back on in order to see which one you are deleting). Do not check the Manual Draw checkbox. Use the Manual Draw checkbox when you want to manually add rectangular APs instead of square ones.
I suggest that you trim your workflow to the bare minimum. Don't worry about Newton's rings, don't worry about flats. Avoid extremes in any direction for any of the camera settings. Get a good image out of AutoStakkert first, then you can start adding the changes back in.
Keep a record of what you did and post the results when you need more help