right so I've sanded absolutely everything back to 400 and now I'm looking to make the necessary adjustments to the scale length.
First off, I've remeasured and at the moment it looks like it is 312mm from nut to 12th and 321mm from 12th to bridge on the low e saddle wound all the way forward with the neck pickup in, with the neck pickup out the measurement sits at about 318mm and I did some measuring on the pocket and neck heel and it looks like taking about 2mm off the neck will allow the heel to reach the back of the pocket
My question is, which part to take out, either the top part which is actually hitting the pickup surround and stopping the heel from making contact as pencilled in here:
Click image for larger version. 

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(it's just that little rectangle and the pencil is a rough approximation)
or, should I file that entire face back so its uniform and a bit simpler and leaves a bit more space in the cavity?
Thanks for your input this obviously isn't something I want to rush into which is complicated by the fact that the only files I've found around the place so far seem to be large bastard files which I don't want to put anywhere near my guitar