I have an a6 block mated with a z6 head, using a z6 intake manifold and z6 hard water pipe (it's got an extra fitting vs the A6 one for a coolant line for the EACV).
My problem is that the coolant is not circulating. The upper rad hose gets hot, but the lower hose stays cold.
Another possibly related problem is that the temp gauge doesn't read.

I've replaced the thermostat (the one I replaced was 2 months old and worked perfectly before on the stock z6) but the problem still persists.

Is it possible that the wrong headgasket was used? I'm not sure at the moment which one was used (I didn't build the motor, someone else did) but is there a gasket that blocks some essential passages? If there are, then maybe the temp gauge sending unit isn't in coolant either and that's why it's suddenly not working.

Or maybe I have a large air bubble/lock? I get a steady stream of coolant when I crack the bleeder screw by the upper rad hose elbow.
I've also taken off the highest coolant line, which is a smaller one that goes to the top of the intake manifold right where it meets the head. There is also coolant there.

The heater works perfectly also if that helps.

 

Compared that pic to my used Z6 headgasket and the headgasket is on correctly.

Also tested the thermostat I swapped out thinking it was bad and it opened up at 180 deg F so that rules that out.

 

was the thermostat in the housing the right way round? thatll stop it circlating, Sounds too obvious I know but possible as you didnt build the motor.

other things to check thinking off the top of my head...
*condition of water pump/does it spin freely?
*was cooling system fully bleeded to get all the air out?

 

Yes there is only one way you can really install it, the thermostat is too long to install it backwards.

Water pump is a used one but was inspected carefully before installation.

I've bled the cooling system using the bleed screw right by the upper rad hose.
I also took off the highest coolant line on the intake manifold to see if there was coolant and there was. I didn't do this while the engine was running though.