Not sure what you call "dead wood" on this one but the roots are very nicely wrapped on the stone.
When properly treated, maples can heal rather quickly: that's why a Japanese maple with "dead wood" looks very un-natural most of the time (except perhaps in some parts of Britain, in which case it can become a "style").
If the "dead wood" is what I outlined in yellow (1), I'd carve out this part and repot it in a bigger pot to let it develop next year: the wound will heal, and the tree will have a better taper. Don't know if the dotted line is a dead root (2), I'd keep it for the moment. Numner (3) is definitely to be removed.
Only when the tree has been cleaned that I think you can imagine a future for it.
You wrote: "repoted 2-3 years ago on river pebbles". Here, they're very calcareous, and yours looks like that too.
Japanese maples resent basic soil, so be careful...
But to me, it has a great potential, I wish we could live near enough for me to take the ferry, drive to your place and help you work on this one.