Hi Sean, I made a rig consisting of a Pentax K-3 digital camera, a macro lens (with extension tube), a film-holder to hold a negative-strip, and a diffused light-source behind the negative. The light is an LED-panel with an opaque white food-bowl over it. All this is mounted on a wooden board. Like you, I couldn't get the colors right. It turns out that there are cross-channel effects in C-41 which the printing-process removes. In a scan, you must remove them digitally. Note that when taking pictures, set your camera's white-balance to "daylight" or "5500K" or "none" for the correction-method below to work properly.
I use Gimp (free download) to edit photos. Here are the steps I use to fix the colors in Gimp: Use the Curves tool (Alt-c c) to multiply all three channels by about 75%; the purpose is to prevent the following additions from clipping at 255. Use the Channel Mixer (Alt-c o x) to add 40% of the red channel to the green channel. Then add 40% of the red channel and 20% of the green channel to the blue channel. I wrote a Gimp plug-in to do these steps; I can send it to you if you wish. After doing these steps, you still need to set the black-point and white-point of each channel based on its histogram (Curves tool). After this, it only takes a little more tweaking in Curves to get the picture right.
Good luck,
Mark Overton