Unfortunately, on non-electronic boilers, labels are all over the place, and the thermostat is reversible -- it doesn't matter which wire coming out of the thermostat is connected to each of the two terminals on it.
The basic principle of how the furnace works with a dumb thermostat is:
24V Transformer (R) ---> (wire 1) Thermostat (wire2) -> Relay -> 24V Transformer (C)
It will also work with the following configuration:
24V Transformer (R) -> Relay ---> (wire 1) Thermostat (wire2) ->24V Transformer (C)
So the first challenge is to identify the (R) and (C) terminals on the 24v side of the transformer.
From there, you need to trace the (R) wire and see if it goes to the transformer first or the relay first.
If it goes to to the thermostat first, that's your (Rh) wire, and the other one is your (W) wire (you can check this with a multimeter again -- at the thermostat one wire will have voltage and the other won't).
Find the other end of the transformer and attach the (C) wire to it as well as to the Nest's (C) terminal.
If not, you now have your (W) and (C) wires -- find the (R) side of the transformer and attach your wire to it. At the thermostat, plug it into the (Rh) terminal.