Hi Lee,
The DAQ PCB v2.01 connects to the CMOS PCB through the J6 connector on the DAQ PCB. J4, J5, and J3 provide customizable digital input/output channels for synchronizing the Miniscope system with other external systems.You cannot connect the CMOS SMA jack to J4.
Yes you can solder the inner conductor of the coax cable to the middle pad of J6. Make sure there are no shorts between the inner conductor and outer shielding of the coax cable before you power everything up.