I'm a wee bit busy to be able to answer your entire post in depth just at the moment, but thought I'd just chip in and give you a heads up on capture sharpening.
In a nutshell all cameras introduce a degree of softness into an image - firstly due to a glass filter that covers your sensor that (amongst other things) attempts to stop a phenomenon called aliasing (a "beating" type pattern where some repeating pattern in an image just happens to resolve to a size that's similar to (or "sympathetic with) the spacing of the pixels on the sensor). So they blur the image slightly with the AA or anti-aliasing filter), god bless them. Additionally, the demosaicing process introduces additional softness.
Capture sharpening fixes up these little anomalies pretty well. Without getting into lots of theories - Canon recommend applying a USM (UnSharp Mask) with the amount set to 250 (or 300), Radius to 0.3, and threshold to 0 (or 1) for 100/200 ISO images - or threashold up to about 6 or 7 for particularly noisy/high ISO images.
If you don't capture sharpen then you won't see any difference unless you're printing really large, and looking really close - but - it makes the images so so so so much nicer to work with when you're zoomed in to around 100% (pixel peeping).
To see the difference it makes, open a RAW image in PS - zoom in to 100% - open the USM dialog box - dial in 300/0.3/0 then toggle the preview control to see what difference it makes.
If you're shooting JPEG then the camera will apply a degree of sharpening to the image - unfortunately (considering optimal sharpening requires at least 3 passes - Capture - content/creative, and output sharpening) the one-size-fits-all default sharpening applied by the camera to a JPG is NEVER optimal - one of the main reasons I never shoot JPEG, but that the subject of a whole new post!
Hope this helps,
Cheers,
Colin - photo.net/photos/colinsouthern