Before Installation

Just scrap everything in the settlement and Transfer Settlement.
There may be some things you need to manually scrap even if you use Scrap Everything, for myself this included 2 dirty window decals where the Red Rocket was and a nest in the air near there as well.

After Installation

Use Workshop Workbench Marker or any mod you may have that moves the Workshop Workbench to move the Workbench to wherever it looks best.

You may have to use SOE pack to place the water in the pool. The water didn't transfer when I tested it but it may for you, just make sure you have dirty water in your inventory. Or you could use Build Your Own Pool to place water, whichever you prefer.

If you used Not Your Average Neon and don't like the power line coming out of the signs, you can use console command to get rid of them.
Press ` on your keyboard, click on each wire with your mouse and type or copy paste this: modpos z -250
That will push them into the ground and out of sight. 250 should be more than enough, if not just do it again.
Do the same with the generators and you will have a clean settlement with no wires and no visible generators.