> Yes so don't I need to input the clock signal from the Beaglebone Black into the Link2?
Check out the I2C spec., e.g. at Wikipedia.
I2C uses 3 connections, SDA (serial data), SCL (serial clock) and GND. This clock (SCL) is a I2C bus signal, and not directly related to the core clock (but derived from it).
Be aware that both signal are bidirectional, more or less. The SDA direction is switched for the ACK bit in every transmission, and SCL can be held down by the slave for "clock stretching" (if supported). My point, trying other non-I2C signal pins might damage the hardware.
> If so I need to do it via a test point on the Link2 but none of them are labeled.
Those test points are for production tests only, not for application use. This is why they are not labelled. They might be labelled at the PCB layout plan, which is part of the schematics.
> I believe both have logic levels of 3.3V.
I would better make sure. A 3.3V level can definitely damage 1.8V electronics, at best you just don't get it to work.