Basically I bolted the neck on and measured it that way so the neck would be stable when measuring. It seems to fit fairly well in the pocket from what I can tell. I'm wondering if they make longer saddle screws to allow me to basically scoot the saddles up by about a 1/2". I have plenty of room for that on the bridge if those are available.
If I carve out the cavity enough to move the bridge I will have to also cut away a portion of the pickguard because the bridge will overlap it if moved into a correct position, though to be honest I don't have the tools to do either really. Main reason I went with a kit guitar as my access to wood working tools is very limited.