I hope it doesn't appear too insensitive to offer a warm welcome to the CameraLabs forums when you apparently have an issue with hot pixels! It's also nice to welcome another budding astrophotographer.
If you haven't found it yet Christian Buil has a great feature here
about using the 40D for astrophotography.
Here's a 2 minute dark frame I exposed a while ago at ISO 400 which you can possibly use to evaluate the performance of your camera compared to mine. It's a 9MB download: Broken link
. There will always be sensor noise at such long exposures so in my opinion it is important not to confuse this with hot pixels which will be significantly brighter than the background noise.
You might like to have a look at my post "Comet Holmes
". The first image was taken at ISO 1250 with a three minute exposure. You can click it to view/download the 100% image. There was a tiny amount of post-processing done as described in the post but the dark frame was not
used. However, I did take one so if you want to download it the ISO 1250 three minute dark frame CR2 file is here: Broken link
I wouldn't advise using the camera's own “long exposure noise reduction”. Not only does it double the time it takes for each exposure but it doesn't give the sensor time to cool down between the light and dark frames. If you are taking a sequence of exposures then perhaps one minute between each exposure is a starting point. The same would go for the dark frames and I would also suggest that you don't need to expose as many dark frames as lights unless you are really on a mission!
EDIT: Downloadable "dark" frames removed from the server.