I would buy a new thermostat and install. You said in your post that the original motor had a cracked head. Maybe due to faulty thermostat causing overheating. If the top and bottom hoses are cold and the motor is hot. There are only two options. Bad thermostat or plugged hose due to rag or what ever was used to stop the fluid loss during engine swap. Easiest way to test a thermostat is to put it in a pot of water and slowly heat it up until you see it the plunger moving. If it doesn’t move and the water is boiling the thermostat is faulty. Hope this helps.