Hi Plainfaced, yes you are correct the screw holes in the body are pre-drilled but the neck isn't. Some necks will be snug and some have a bit of movement in the pocket. The best way to drill the neck screw holes is to install both E tuners, fit the bridge and string up both E strings. Then clamp the neck so both string to edge of fretboard offsets are about the same. Then drill the neck screw holes.
Keep asking questions it's the only way to learn and the forum is here to help.
Worth having a read of Gavmiesters fret levelling post he linked above







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