Hi Stephen, I would watch these videos to help you put it all together.
http://planetaryimagingtutorials.com/
1000 frames is far too few - You can capture for 3 minutes on Jupiter without getting into problems with planet rotation, and you should be able to image at >100fps easily with your system. Try 1 minute per filter and you should get lots more frames to work with.
I only capture in colour with an ASI224MC, and on my last capture (see images in the Solar System Images forum) I took 27000 colour frames and stacked the best 7500 or so.
Watch the videos above, you will learn a lot (at least I did
).
Andrew