How is it now? Did the poly completely harden? I can't remember if you mentioned which poly you're using? It occurred to me that you might want a protective "cap" between your stain and your poly, or between your filler and your stain, or both.
If I used a water based product over another water based product, I will generally put a cap of platina (a.k.a. ultra-blonde) shellac between them. It's almost as clear as a water based poly, it will stick to almost anything and almost anything will stick to it. It's also cheap and dries fast. Since I wipe or brush on everything but solid color paint, I end up using it a lot to keep water in top coats from activating the water in under coats. Although I don't tend to use oil based finishes, lots of people use platina shellac to guard against compatibility issues between products. Just a thought...