when I work digitally from sketches... I normally only use the sketch for a guide only... so I scan it as grayscale... adjust levels in
PS to make lines dark black and bring back white background which gets rid of some smudges and erased lines... then just lay that in background of
PS or AI and work over top.
It sounds like you are spending a lot of time preparing your scanned sketch in order to save time by using "live trace" in AI... is this correct? Why not spend less time cleaning up scan and more time just tracing manually? I am a bit old school (just don't use much of the new features unless it really saves me time) and that is way I have always worked.
Also, consider your needs for final output of your image. Is the final image all vector? I ask because you mentioned coloring in PS. If the final image output is not a .ai or .eps vector file... I would skip the AI part totally. This would allow you to to probably recreate your more illustrative look easier in
PS that would likely more resemble your drawing IMHO.
Below is one of my projects in which I created in AI. I had scanned each cell of the illustration from larger rough pencil sketches and the recreated in AI just by manually tracing my sketches large and reducing and coloring in AI. Had my original drawings been more detailed... I might have just done it all in
PS but my sketches were really quick and rough and I didn't know how many projects the art would be used for so just worked it all in AI while trying to keep the illustration effect....