Thanks for your comments.
I'd prefer to remove material from the bottom, since the top is already compensated and it's my first go at fixing action and intonation and I wouldn't want to change the compensated saddle at this stage.
I first want to get the action set according to my measurements (truss rod already adjusted).
after I get the action correctly, I'd deal with intonation compensation.
So bottom part of the saddle is where I'd like to fix the issue.
I'll try applying more pressure where the high E is located and use only one forward motion when sanding.
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