In the switching doc and the build guide for the Choral Reef, Brian indicates that C6 should be inverted to create a separate bias rail for the MN3008.
Your V- pad should measure 5v.
In the Choral Reef the following exceptions are applied. - - - - R5 (8k2) and R6 (10k) are only used in the Choral Reef. These resistors are left off in all other VFE projects. IC2 AND C5 are also left off in the Choral Reef. C6 is still used, but it should be installed backwards. IOW, the + side of the cap goes to the round pad on the PCB and the – side to the square pad on the PCB. The V- pad on the switching board is still wired to the V- pad on the Choral Reef audio board. But, in this case it carries approximately +5v to the Choral Reef audio board instead of -9v that we would have when using the charge pump. This is to give the CF board a separate bias rail it needs to operate properly.