If you haven't already guessed, the blue pair in a cable is the first line and the orange par is the second.
The reason for 3 wires is that one jack is feeding another one or two jacks somewhere else in the building. If you carefully tag the 3 cables that go to the jack, you can remove one at a time until you don't get dial tone, or remove them all and put them back one at a time until you get dial tone. That is the feed pair to that jack and if you search, you'll find that 2 or more other jacks are now dead.
The trick is to find the closest jack to the demarc and hope that it is the one that feeds dial tone to the whole building. Get out your toner and probe and start testing :-) or just do it by trial and error.
When you're finished, you'll bring the second dial tone into the building on the orange pair and wire that orange pair to the black/yellow wires on the jack. If you need to send that dial tone to another location, you'll need to put 2 or 3 pairs down on every jack just as they did with the first line.
I would guess that the reason for the orange pair is because the previous tenant either had DSL, or a broken blue pair on that cable.