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I am putting this motor together and I noticed that the two wires one purple one purple/yellow, these are the thermo sensor wires that come from the engine near the third coil, these are missing. 'Will this make a difference in how it runs?
I'm looking at a factory 77 manual which usually is pretty close, and I don't see the wires you mention. The brown wires are for the head temp switches. The purple with white tracer is for the choke solenoid. The purple is hot to the key switch. Sorry that this information is not more helpful. You will have to get hold of the specific 76 factory manual and check the color wiring diagram in the back.
There was a service bulletin saying to disconnect the choke thermal switch. So you don't need it and don't worry about it. You should have two wires coming out of the choke solenoid, a purple/white and a purple/yellow. Connect BOTH of the wires from the choke solenoid to the purple white coming from the choke switch in the control. Disconnect the wires from the thermal switch if any are there.