Overworld portals that are within 1024 distance of each other on both X and Z axis are almost always going to link to the same Nether realm portal on initial construction because 1024 translates to a distance of 128 in the Nether Realm, and the game checks for existing Portals within 128 "radius" around the destination (the 257×257×128 box).
What is the best way to still allow BOTH portals to exist, but make the NP#2, be the portal that is "primary" in that when leaving the Nether we will arrive at NP#2 instead of NP#1?
I thought of another idea, but would this work. The other portal (the one which is the primary one) is within about 800 X distance from the portal #2 in the overworld.
NP#2 is at -519, 77, 201
If we go to the Nether, then build a portal while in the Nether at location -65, 77, 25 will that link it to NP#2 or would that create a brand new portal?
Question 2 sounds correct. The easiest way to resolve 2 overworld portals linking to one nether portal is to find where the second nether portal should be and create one manually. Your math looks right so it should work, although elevation doesn't matter with Nether portals really. Just find a place to put it at the X and Z coordinates.
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If the portals are close enough the elevation does matter, though it sounds like the portals in question are far enough apart that it wouldn't matter.
When you enter a portal the game calculates the "proper" coordinates in the other dimension and looks for portals within 128 blocks horizontally, if it finds more than one it sends you to the one that is closest in 3 dimensions (except that you can't go to a portal above Y=128 in the Nether.)