Leave it as it is. The important thing is that the flat surfaces are flat. If you've got dips in the wood, then it's a lot easier to aggressively sand the wood now to get the body flat, rather than have to apply lots of coats of clear in order to fill the hollows before you can then sand the clear coat flat.
Sometimes it's worth sacrificing a bit of stain and apply another coat just to sand the flat surfaces lightly with sandpaper stuck to a long flat piece of wood just to see if there are any significant dips where the stain isn't being removed. It's almost impossible to see this without the surface being stained or having a light mist coat of a darker colour sprayed on. It's so much easier to do this at this stage than after putting the clear on and then hoping you don't sand through the clear when getting the finish flat.
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