Though I don't print from Kicad, but I can give suggestions from gerber viewer, Pentalogix's Viewmate. 1. You can create gerbers from KiCad 2. Import layers into Viewmate where you can change the layer order and set colors, then print into PDF. At last, s

I guess what you are using is the standard Kicad library. You can find the reference designators on the silk layer and the values on the fab layers. So you need to select these two layers when printing.

I notice that layers are set invisible in the layers tab are not printed even if they are selected in the print Dialog.