Matt: Here's something that might make the process easier. If the pdf has layers in it, you can limit which ones display in the pdf at any time, and save that as a jpg and only those layers will be in it. This can reduce your clutter considerably when using ArcScan. If you have a lot of layers you might even turn on different layers and save to jpg for use in Arcscan.
In addition if you have a color pdf you can convert it to grayscale, then save it as a pdf, then when you open it in ArcMap you can use the classify option and limit it to 2 classes, and then make the "white" one no color.
I would have thought that by now there would have been readily available software to convert the individual vector layers of a pdf to a vector usable in other programs, potentially even georeferenced vectors, but I can't find any. I saw suggestions of creating eps or wmf files (you could use Adobe Pro, Inkscape) and then opening them in ACD (formerly Denebas) Canvas, but I don't have the latter. Maybe some other user has more information on doing this.