What do you use silk touch for?
I'd suggest either:
- Move portal 1 up to a higher altitude in the overworld, until it can connect to the horse road portal.
- Demolish your portals in SKA and start over, placing them in the order you consider them most important in.
The problem is that many of the portals in the nether are at low altitudes, that causes conflicts with portals that are high up, when they're all at low altitudes in the overworld. The portals want to connect to whichever is closest, and y coords are taken into account there.