As stated, try bleeding the cooling system from the header tank on top of the inlet manifold. You need a container that will seal in the hole where the cap goes, half fill it with coolant, then with A/C off run the engine till the thermo fans kick in, let them cycle and go off. You should see bubbles coming up through the coolant in the container. give it a couple of revs to get all the air out. Remove the container and put the cap back on. fill the reservoir over the full line by about 5cm as it will suck coolant in when it cools down. If that doesn't fix it( can't really see why gearbox repairs affect the cooling system anyhow) Then you need to pressure test it for leaks, or it may be a blocked heater core.

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F.B. Racing
01 WRX (STI badged)
2010 XR5 Focus
06 Impreza Hatch 2.0i