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What year is your Cougar? Some use two Vehicle Speed Sensors (VSS), both near the output of the transmission, one feeding the Powertrain Control Module (PCM), the other the speedo/odometer. Other models use a sensor built into the speedometer cluster.
If it's running and shifting normally you're probably just dealing with one loose or disconnected harness. Look around the transmission output. If you see two connectors one of them is probably loose. Unclip, clean & replace.
If you see something like a wiring harness coming out of the speedometer cable (how it's been described to me) then you might have a loose connector in the cluster, though this would make it run & shift poorly. That part is beyond my anecdotal knowledge.
Disclaimer: I haven't worked on either version.
Are the replacement engine/trans the same as original or a year/performance swap? I've heard of some combinations that cross years that required extra work due to sensor and computer changes.
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