For removing wax, I use 91% rubbing alcohol on a soft cloth. Note, this will also remove gunk from the bowl and also a bit of the stain. Go easy, go evenly.
Now, granted, the only time I'm removing wax is when I'm completely restoring a pipe. Just keep that in mind. I've also found that polishing will put a bit of the darkness back into the coloring, thus evening the process out.
If the wax is very resistant, you can use the above method with some superfine steel wool (#0000). Again, this is more aggressive than the cloth, so you'll probably lighten the color even more. Steel wool can also be used to even the color out in case of splotchy coats. It's also a great way to remove very minor scratches and even put a slight sheen to the wood.
Now, for polishing and waxing the standard method is white diamond (1st) and carnuba (final) used with a polisher at about 1750 rpm. Not everyone has the equipment, so
Paragon Wax is the next best thing for smooth pipes. Put it on, let it dry, buff it off, then do a final wipe with a nice, clean, soft cloth. I use an old shoe brush that is super soft from age, and get a mirror shine.
Hope this helps. Perhaps someone here knows a method of removing the wax without lightening the stain color.