Personally, I don't like to use a water-based clear coat over a water-based stain. I've found that the color migrates from the stain into your polycrylic, so if you try to sand the poly-c at all you also sand out some of the color. The result is either a not smooth finish, or an uneven color. I think it's a huge hassle.
I like to use a water based stain, with an oil based poly on top. This way, none of the color migrates, and you can wet sand the clear coat without affecting the color.
I've found there isn't much benefit in really fine grits before applying a water-based stain, as even if you pre-raise the grain, the water based stain still raises the grain again. I haven't found much benefit to pre-raising the grain. It sounds like a perfect solution, but it's not been effective for me.
As always, experiment on scrap first.