Finally got my portals working two-way. Side product: 98 free Obsidian.

So I spent countless hours digging this cavern to make the game actually spawn the portal from my main base into Nether correctly.

It kept spawning a portal and when I went back into it I always ended up just outside of my base. I did that multiple times (trial and error) and ended up with 4 trash portals just outside my doors (or on top of them).

There were 3 trash portals in the Nether so that totals 98 Obsidian. Too bad it'll take 24½ minutes to gather it all back up :S