How should I wire this White-Rodgers fan and limit control? What about the thermostat?
Here's the installation manual for that thermostat:
http://www.emersonclimate.com/Documents/White-Rodgers/instruction_sheets/0037-1558.pdf

You're right about L1 and L2, and about it not mattering which is which inside the thermostat housing.  It is a single throw switch so its terminals are interchangeable.

The yellow triangle labeled "2" in the diagram is any device you want to turn off when the temperature gets too high.  The installation manual uses an oil burner as an example of such a device.  In your case you'd leave that switch unwired, unless you want to rig up a solenoid valve to douse your wood fire.  :)