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The horizontal lines may go with darks and bias frames. A dark is simply a shot with the lens cap on for the same duration as the light exposure.
Usually you take at least 6 and median combine them or sigma reject combine to make a master and then you can use it every time you take the same length image. Best done with Images Plus and use what is called adaptive darks as the temperatures the images are taken at will vary and the dark noise is thermal noise and is worse when the chip is hotter. Adaptive darks takes that into consideration.
A bias frame is simply a very very short exposure - say 1 second which shows the noise generated by the reading process of the camera. This may show the horizontal lines (a guess).
Also a flat which is where you take an image with the same setup you took the light exposures with (same focus and orientation of the camera exactly) and at dawn or dusk. About 3 seconds to get a not too bright image which is a picture of your optical system's imperfections and uneveness of brightness. It will also pick up dust particles on the chip of the camera.
Normally you subtract your bias from the flat and then the flat is applied to the light along with the dark. This process is called callibration or callibrating an image. If you don't change your camera's position then that flat is valid until you do.
It is often amazing how much it will improve an image.
In your case 40 minutes is not that long so your stretching is showing up the noise that has not been dealt with above that is normally a bit hidden until pushed.
Greg.
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