After the wedge is in place, you can see how much it angularly kicks the neck up out of the body.
I mark a line as to where I need to remove some wood from the neck.
Then I cut that pencil line on a bandsaw. I left the line a little heavy so I could sand it down. Please ignore the rude thing that wiener dog is doing in the background.
Now the neck lays into the body just a hair high for sanding it flush. You can see bandsaw marks across the thru-neck but those will all be sanded away after it's glued in place.