One problem with water based color coats is that they open pores and raise grain to the point that sanding through it is almost necessary to achieve instrument/furniture grade smoothness. The other problem is that they don't sand nearly as well as the hotter solvent products. So even though they require an extra coat and more sanding, they don't sand as well or as fast. That isn't to say that you can't get an acceptable finish from waterborne products, but it's more work and, if there are flaws, you may question if you could have done better. You probably could have.?. There are two component (catalyzed) waterborne finishes that are being used by bigger manufacturers and the automotive industry, but the typically require special equipment, care and expertise to get the most out of them. Maybe worth looking into depending on how far you are willing to go to avoid hotter solvents.
So, I would look into single component waterborne auto finishes. They are out there and they have a mixed rep for cars, but should prove plenty durable enough for a guitar (ie: not travelling down a hot, sunny highway at 60mph or sitting out in the rain for weeks ) You'll still need some good spray equipment and an empty space that you can turn into a clean room (filtered venting preferred).
Good luck. I too hate the hotter solvents. I deal with them on an as needed basis because I have fewer problems and less time getting to the desired result.
EDIT: This assumes your parts aren't already primed/filled. So I would assume the waterborne criteria applied to any primer/filler also.