On my '87 300E w124, the wiring for the 3rd brake light runs inside the trunk, between the metal of the parcel shelf and the fabric of the parcel shelf. It leads to the drivers side, and comes out with several other wires (Trunk light, speaker wires?) by the drivers rear speaker, then goes between the trunk liner and the rear fender near the power antenna. Hope this helps, but am curious why someone would remove the 3rd brake light.
2003 Firemist Red/grey leather SL 500
2015 Palladium Silver/black mbtex GLK 350
1987 Smoke Silver/burgundy mbtex 300E Sportline (SOLD)
Click to see 87 300E