Are there any Male to Female DI2 wires / exetensions? I know you can use a junction port (ie: SM-JC41 Internal Junction Box B) for this, but are there any Male to Female extension cables?

Root Cause: R600 to 5 port junction for a TT setup near the base lever (Magura's so can't use the standard integrated TT brake/shifter)
No, there are not any male-to-female "extension" wires available for the Shimano Di2 E-Tube system.  You can use a junction as you said, or you can use the two-port ANT module.  You could also modify an E-Tube wire to lengthen it yourself, if you are handy with a soldering iron.