Logically, the distance between the bridge and the neck needs to be reduced. Either that, or use a different scale neck with that body, or vice versa. Or the guitar will never intonate properly. That's what I'm seeing.
Can it be done with that body? In theory, I suppose. But if you cut the neck pocket deeper, would there be some negative repercussion that you're not aware of? You'd be removing wood between the pocket and the neck PU rout, making it thinner in that area. I have no idea if that would be ok.
Or, can the trem posts be drilled a little closer to the bridge PU cavity? Again, how close is too close?
A combination of both adjustments?
I'm sure Andy will know what to do...