My 2c - my experience (graphic arts business) is that, like analog image capture, you are fitting a range of values (and colors) into the range of another medium, which, in this case has 256 values, including both ends. In analog film work, you do this by finessing expose and development, as is discussed at length on this forum. The same is true in scanning - you are fitting a range of tones into a file. The closer you come to filling up the range of 256 values, the better the separation you get between adjacent mid-values.
So - my approach is to scan manually (I use the Epson SW with a 4990 also) set the sliders in the levels to just include both ends, with a small amount to spare (the densitometer tool can help with this). Then I scan to open the file directly in Pshop, tweak the end points, and adjust the curve if needed for middle values to the print, and save in Pshop. Also, remember that you are adjusting mid tone values for your display, so, when others are viewing your work in the gallery, they may not see what you are seeing anyway.
Cantore's last question - I like to scan for 300ppi at the print size, or slightly larger, then resize the scan later to APUG gallery guidelines.