I trust my camera, but only to a certain point. I just learn the limitations, and where it starts to no longer function quite as desired, and then figure out a workaround if necessary.
Granted, I have a 5d3, but was shooting a 5d2 before. Really it comes down to experience with your equipment, regardless of what it is. Once you have the requisite experience, and know the strengths and weaknesses, you have trust that you can get the image you want with what you have. It sounds like you've shot a lot of photos, but have you really thought about what you are doing and why during certain types of subjects and situations you are photographing? Have you tried shooting one way, then shooting a different way in similar situations and see if one way gives you better images (subject to what you consider a better image)?
One thing which would help you (if Canon would implement it) is AFMA which can help avoid AF misses due to slight front/back focusing problems. Your idea to take multiple shots is a good one, especially if you are working with a low shutter speed since your 2nd or 3rd photo will likely when you are in a more stable position, instead of slightly moving the camera as you press the shutter button.