I am left-eyed and have a few M6's (I'm not sure how big a difference the form factor is compared to an M9). I actually enjoy focusing with the RF, especially the big bright view in the RF window. The only drawback with being left-eyed and using an M6 is that I have to move the camera away from my face to wind the film. It's just part of my process with the camera now, but obviously not a consideration with an M8/9.
Depending on the situation I either zone focus with smaller apertures, or if shooting wide open (which is most of the time) I focus then recompose if necessary. When forced to focus/recompose I try to focus on something that's close to the plane of focus as my subject, always aware that this involves compromises. Instead of shooting a burst like with a (D)SLR, I just keep the camera to my eye, focusing/refocusing, composing/recomposing until I think something good is happening or going to happen and click.
Missing focus is generally due to pretty obvious reasons: I didn't focus on the right spot, either me or the subject shifted, or due to recomposing. But then again, I miss focus using a DSLR with AF too. Nothing and no-one is infallible, especially when you're rushing or careless. You just have to learn the quirks of the system you're using. In fact, I would say the M is a camera you should use to the exclusion of everything else for a while to truly become comfortable with it. Not because it's "harder", but simply because it's different.
Everyone seems to want to get perfect sharpness out of the M lenses, but my opinion is that the M rewards wide open shooting with minimal light (bright RF, "gentle" shutter), so you are most likely trading off optimal sharpness in these situations anyway.
There is so much BS surrounding the Leica M. In my experience, yes, it's slower and it does make you think and work differently. This is all part of the mystique/quirkiness/joy/frustration with the camera. Whether it shows in the final result or not is up to debate. Whether anyone finds it more "rewarding" to use is up to personal preference. Personally speaking, I love shooting with the M, but contrary to all the Leica fondlers and haters, having a red dot doesn't make the camera or it's lenses automatically magically better or worse than anything else.