Pete:
Running your engine without the air vanes and thermostat will cause it to come up to temperature very slowly and then continue to rise in temperature to something higher than if you had the vanes and thermostat in there. They actually make the engine run warmer when it's cold out, and cooler when it's hot out, especially Cylinder #3. In other words, put them in.
There is a set of those flaps on both sides (left and right) of the fan shroud. They are connected to each other to work in tandem with a flat metal arm that connects between them across the back of the fan shroud. All interconnecting stuff is held together with special springs, flat washers and spring clips to hold it all together while not binding anything.
They should all work very freely when assembled and connected (no binding) before you connect the bellows thermostat. If they bind, find out why and correct it.
Install the bellows actuator arm (a short, bent rod) into the passenger side flaps (there is a little loop in one flap to receive it) and then aim the rod down through the appropriate hole between the cylinders as you seat the fan shroud (you'll see it - it's pretty obvious) so that it protrudes from below the cylinders. Again, it should not bind in any way.
Once you get them installed (use 8mm screws and lockwashers) then spin on the bellows finger tight and assemble the mounting bracket to the case but don't tighten it yet and don't put in the screw to mount the bellows to the bracket (yet). Open the flaps fully, loosely assemble the mounting bracket to the engine case and move the mounting bracket up until the upper part of the bracket just touches the top of the bellows.
Lock the bracket into position, then pull the bellows down to seat into the bottom of the bracket, install the mounting screw and tighten. The bellows is keyed into the mounting bracket such that it cannot unscrew itself from the flap actuator rod.
BTW: I have NEVER built an engine without ALL of the original cooling tins, air vanes, thermostat and associated cooling stuff properly installed. I've also never had an engine overheat.
gn