hey there - hopefully you figured this out. The 4CM works well, but I still can't understand exactly how :P . The best web site outlining how cables should be setup, IMO, is here: http://guitargearfinder.com/guides/use-four-cable-method/. You can absolutely do what you've described. First off, it sounds like you want the order of the banks reversed (most use 1>2>3>4). There's an option for this in the setup menu. And then you can also insert the FX loop at any point in the M13 signal chain, so after all 4 banks, or after just 1, or 2, or 3. This gives you the option of running delays and modulation, etc., only after overdrive and distortion have been applied, either using other pedals or the front end of your amp.
For your last question, I'm not sure you can do this. But everything else is feasible. HTH