Hey Budi,
make sure the neck pocket is free of any dirt or steel wool shavings to ensure the neck is seated flush with the body - ie closest to the bridge. I'd put the neck pup in when you do this to make sure it fits ok.
Usually the bass (wound) strings need a small compensation for the width of the string so generally the 12th fret to saddle distance should be about 3-4mm further on the wound E string. As the bridge is fixed with the posts drilled I'd glue your neck in (once you have tested the neck pup fits). Make sure you get the neck alignment correct while gluing, have both E strings on to get the offset of string/fingerboard edge fairly even.
I think you should be able to get the intonation fairly correct, all LP builds I've done and most I've seen work out fine.
Check the distance 12th fret to treble E string saddle and it should be less than 319 - 324mm as the bridge should be slightly angled to compensate