I made a Portal outside my main base and one outside my Mob Tower, which are quite far away from eachother. My Portal from my Base links back all right, but my Mob Tower portal leads to the same Hell Portal, and when I exit, it's from the Base Portal. How would I link these two so I have a shorter path between the two portals?
Get yourself 10-14 obsidian and a fire starter. Put it on peaceful mode (Or prepare to work fast and/or get frustrated from fireballs).
Count the meters between your two portals. Let's say they're 150 meters (blocks) apart. You don't have to be exact but you should be within 10 or so.
Go through the first of your two portals. The first one you laid down. Make sure you're facing the direction of the other portal.
Don't turn, and walk 1/8th the number of meters you determined above. In this example, you'd walk 150/8 = 19(about) meters.
Build a portal here. Light it, and go thorough.
If you did it right, you will come out in your 2nd portal, and everything will be linked correctly.
Except there is no way to be sure your first portal was correctly placed. Your two overworld portals might still go to the same one in the Nether despite this correction.
The hell? Whichever of his portals was built first, will be appropriately linked to it's proper real world counterpart. The system works THAT much at least.
This bug is caused by the fact that portals search for an existing portal within a range before attempting to create a counterpart portal in the opposite dimension. However, this search range is the same in both the Nether and real world, and thus ignores the 8:1 compression ratio in the Nether. This means a portal will link to a portal that is "close" in the Nether, but actually links to some far-off portal in the real world.
5th Horseman's fix will work, as assuming you build the Nether portal in the correct spot, the Earth portal will find that one before your first one as it is closer to the origin point of the search pattern. Your portals then should work as intended.