Just finished overhaul on 95 civic D16Z6. Ported and polished head,metal gasket,pistons,eagle rods,turned and balanced crank new waterpump etc.
The engine runs fine but overheats with the thermostat in. The lower hose doesn't get warm at all. Works fine without thermostat. We haved tried 2 different thermosats and tested them.

 

Could it be the thermoswitch?

 

maybe you put the thermostat the wrong way..I did it once ..lol..

 

NICE! You should be able to see the dome part when you look through the top neck. Uh... I think. lol

 

It should only fit 1 way, would be hard to put it in backwards

 

Don't run without a thermostat. It can lead to hotspots throughout the engine and subsiquent overheating issues even though the gauge reads normal.

 

Cool. I didn't know that. I still think it could be the thermoswitch. I forgot to reconnect it once, and had this problem.