I'm no expert, but should be fairly easy...by editing one of the default .fx files. .fx files are plain text editable in notepad. Alway work on a copy, not the original file.

Color is controlled by the 2 'color' statements under the [ParticleAttributes.x] sections.

Color Start=40, 0, 0, 1
Color End=60, 10, 0, 0

The values are Red, Green, Blue, and Alpha(transparency). The R,G,B  represent the amount of each color to add to the mix. Values are from 0 to 255.

The above are from the [ParticleAttributes.0]  of fx_navred.fx.  To create a purple light I added amounts of blue equal to the red.

Color Start=40, 0, 40, 1
Color End=60, 10, 60, 0

Did the same in the other [ParticleAttributes.x] sections. Saved as fx_purple.fx to the Effects folder. Attached it to an aircraft and, voila, purple light.

You can download the  FS2004 Special Effects SDK from here.
http://www.fsdeveloper.com/forum/downloads.php?do=cat&id=10