My guess it needs to be potted up with good bonsai soil.
If you've done the white paper test for mites with none showing.
It needs oxygen, and hopefully you've removed the greenery growing on top of the soil.
I wouldn't go all out on the roots when repotting.
Note: repotting is something I do when a tree is healthy and full of vigour.
But when the roots are the problem, it's not going to get better left alone.
Not to say the roots are definitely the problem, and I don't know what shimpaku
looks like with tip blight, but other trees would surely show signs if it were disease
I would think.