Wikipedia has an extensive set of anatomy SVGs, but I not not be able to highlight different organs or parts dynamically, because there are no source files with layers I can manipulate in photoshop or gimp. How can I edit an .SVG file?
An .SVG file IS a source file. It isn't layers in the Photoshop/Gimp sense but it absolutely can be picked apart. Use an SVG editor - that would be Illustrator or Inkscape.
Alternatively, if you want to get real crazy you can open the .SVG in any text editor and look for the values you want to change which for colors would be in Hex format #nnnnnn