Second Nether portal links back to original portal location in the Overworld

Sorry if you already tried this with

"I then calculate the distance and stuff"

but copy down the coordinates in notepad. divide the coordinates by 8. if you get a number like 37.75 round-up to 38 if you get like 37.25 round down to 37. Go to those coordinates that you divided by 8 in the nether. Build a nether portal. Should build a new nether portal or link to the existing one in the village.

Hope this help out!

There's no way in hell two portals in the overworld 5k blocks apart would link to the same Nether portal. Portal linking works by dividing the overworld x and z coordinates by 8 (and retaining y unchanged), then seeking within 128 block radius from the calculated point for an existing portal. 5000/8=625, so even if the linking was as weak as possible, 128 blocks from the 'exact' position towards the other portal, 625-128-128=369, the absolute minimum between the two portals in the Nether that would result from two overworld portals 5k blocks apart.

If you get sent from the village portal 5k blocks apart, to the Nether portal that generated from the spawn portal, you're facing either some server mods, or a severe bug.

Even then the search for a matching portal within 128 block radius isn't fault-proof. Depending on lag and other random factors, a new portal may generate in case the matching portal is within 128 blocks from the perfect point, but closer to '128' than '0'.