Rewiring Swamp Cooler - Electrical Question

I'm installing a digital thermostat on my swamp cooler where previously there was only a six-position manual switch, the normal factory type (high/low fan, high/low cool, pump and off).
Normally, apparently, there are four wires coming from the swamp cooler: power, pump, high fan and low fan. Indeed, the manual of the new thermostat detail how to wire the new thermostat from these four wires.
Well, after much frustration, I cracked open the junction box on the cooler and found that one of the four wires is terminated immediately once inside the cooler assembly, connected to nothing! Now, this cooler has functioned perfectly for years, and I'm wondering how it could have without one of its four wires connected.
Any help explaining this and/or helping me to get the new thermostat working would be much appreciated.
Here's the specs for the new thermostat:
http://dialmfg.com/Technical%20Assistance/Technical%20PDF%20documents/PN%207619%20Instr%20Eng%20123.pdf
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snipped-for-privacy@gmail.com wrote:

http://dialmfg.com/Technical%20Assistance/Technical%20PDF%20documents/PN%207619%20Instr%20Eng%20123.pdf
Could be a single speed fan. Does the fan run at 2 speeds? Or pump goes somewhere else? You could trace the unconnected wire back to the switch to see which function it is for.
-- bud--
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