OK so the R1 and W1 in Picture A go to the outside unit correct? You need to follow these wires and verify where they go.
You also need to find out the source of the Red and White wires coming out of the wall in their own sheath.
I honestly do not have a clue how the humidifier is working. The Yellow wire on the thermostat controls the compressor on the outdoor unit. Being summer you do not need it so that can slide for a while.
If you want to run new wires get a 6 conductor cable: and connect Like colors to like colors on both. Y to Y between the air blower and the thermostat, R to R , G to G, W to W, Y to Y and use Black between the C on the air unit and the thermostat C.
The function of these wires is as follows: Red=power, G is fan, W is heat and Y is AC compressor. C is the common power wire Reference: »
home.howstuffworks.com/h ··· tat3.htm This example has separate Rc and Rh wires. In yours the Rc and Rh are jumpered.
For now leave the odd Red and Yellow wires associated with the humidifier alone.
This will give you basic air conditioning and heat.
More information is needed to sort out the humidifier connection and operation.