Your M42 image shows movement, getting to the source of that movement would be step one. Any movement at that magnification will cause blur. Periodic error, a light breeze or poor seeing conditions could all be a culprit. It's easy to assess seeing conditions through the eyepiece, if the stars in the trapezium are twinkling like crazy you're probably not going to get great clarity regardless of how well focused you are. On a steady night I would start with a very short exposure and slowly increase the time until you begin to see star distortion from movement. Then I would back it down just enough to get those stars nice and round. I would shoot 30 or more exposures like that to stack. If you see movement at 1-15 seconds you are likely getting some periodic error or your alignment is way off. The clarity in your Jupiter shot is very nice but it's also a fraction of a second exposure so it's not apples to apples with your M42 shot.
Also, precise balance of your rig in both directions with the camera attached is very important to how your mount will perform during extended exposures. Learning to drift align my mount and properly balance it had a huge impact on the quality of my images and the ease of acquiring them.
One minor note worth mentioning, shooting afocal adds more glass to the light path and in addition the quality of that eyepiece and the glass within has an effect on image quality. Have you tried long exposures shooting prime focus, removing eyepiece, and diagonal if you use one? SCTs by design are "softer" so removing anything that might compound that can't hurt.
If you have collimated the scope via a star test at high magnification then you can be confident the scope is collimated. I personally would not rely on visual focus on an object to determine proper collimation of an SCT. Even a slight misalignment can compromise detail. Here's a great reference, you may already have it:
http://astrosurf.com/legault/collim.html
I hope this helps in some way.
