Yeah you definitely don't want to do anything to the images before DSS doing its stuff. Use the raw files instead. Debayering a raw image is not particularly computationally intensive.
What consumes most of the time when stacking is the star registration, and the default settings in DSS exacerbate this if you have a widefield with lots of stars (intentionally!). When you go to Register Checked Pictures and the Register Settings dialogue pops up, click the Advanced tab and increase the Star Detection Threshold. For it to work well, you only need about 200 stars, so increase the threshold accordingly. This will reduce (sometimes dramatically) the time taken to process the images.
Once you get the result, it's a 32-bit TIFF file...you will need to bring the black and white ends of the histogram in quite a bit to see your data. That is normal
Once you've got the "luminance" about right, then you can think about stretching the saturation. From an unmodded DSLR, you shouldn't have too much work to do to get the colour balance right.