To complete the build as-is, you will need to first run the included startup.txt BAT file 

This will configure the required overlap tolerance for easy building (specifically needed at this extreme for the grav drive.


IF YOU DON'T WANT TO DO THAT:

You can optionally replace one of the reactors with a lower grade (slimmer) grav drive

Everything else that requires overlapping can be achieved using the flip glitch

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For ease of building it is recommended to unlock all build items to a single technician. If you don't already have this:
Shipyards Unlocked https://www.nexusmods.com/starfield/mods/721
M Class Components* https://www.nexusmods.com/starfield/mods/3688 (*used for the grav drive and shield, so can be avoided if desired)

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Weapon placements are optional as I wanted to try and conceal to them, it's a personal preference.

If you prefer not to do this, the 4 turrets can mount on the top of the mess hall where the portholes are,

and the 4 EM emitters place nicely on the top/bottom of the Deimos wings (this will avoid one of the interior clipping issues)

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The big payoff for this design is that the engines will clip into the rear of the battle stations hab (see images)

If everything is chosen and aligned correctly, you should have a central ladder running through all decks from the bridge down to the docking port