I'm in the middle of doing a cylinder compression test on my 2006 Common rail, but I can not get to the power supply plug on top of the fuel tank, is there some other place to cut the power to the transfer/lift pump?
I unplugged the wire connector to the CP3 pump.

 

I recommend to leave the ignition key off and just activate the starter using a remote starter switch.
This will leave the ECM, CP3, injectors and lift pump with no power (inactive) while you spin the engine.
May sure you have all the injectors out before doing a compression test.

For the 2003-04.5 trucks there is a yellow wire near the engine bay fuse box that is the trigger wire for the starter.

I'm sure there is something similar for the 2006-08 trucks.

 

So I did just unplug the power to mt CP3 pump and then cranked the engine and no fuel came out, but I can hear my transfer pump kick on when I turn the key on.

I still did a compression test this way, seem to work fine.

 

I wouldn't recommend anyone else do a compression test on a Cummins the way you did. I'm surprised you had no fuel come out of the fuel rail while cranking with the ignition key.

The "power" plug to the CP3 high pressure fuel pump is really the FCA connection. It controls the input to the CP3.
With it unplugged, the FCA allows maximum low side fuel input to the CP3.

Regardless, the compression test readings should be 300PSI+ for each cylinder.