As is obvious from the above I am not an intonation expert 
But it was really not too difficult, just a little time consuming. You might need a good tuner though.
Basically, what I did was repeat these steps. These will only work for basses with intonation screws on the back of the bridge for each saddle, which is common but not universal.
- Tune the open string.
- Play the 12th fret harmonic and fine-tune again if needed.
- Play the fretted note at the 12th fret.
- If the fretted note is flat compared to the harmonic, shorten the string by moving the bridge saddle closer to the headstock. On my bass, this means “loosen” the intonation screw for that saddle. This may be different on your bass. Take care not to loosen too much if your saddle is near the end of the screw.
- If the fretted note is sharp, move the bridge saddle away from the headstock. On my bass, this means “tighten” the intonation screw. I recommend detuning the string before you do this to ease tension on the intonation screw.
- Tune back up (important, changing the intonation will also change the tuning a bit) and repeat until the string is intonated correctly.
It turns out Marcelo has a video about this too, which I should have searched for before asking at all. He explains it all really well.
His other setup video is fantastic too, do it first before intonation:
Basically, to set up the bass, you want to do things in this order:
- Adjust truss rod if needed
- Adjust action if you want
- Set intonation if it is off