Snake, the rule you quoted says "... passengers may standby on same dayflights after their ticketed departure timeonly if they have cancelled their reservation prior to the ticketed departure time." (I just love the lower() function in Excel), and that is exactly what PrivatePilot did.
PrivatePilot, you are due the originally booked EQM, since you abided by the rules of the fare as posted above. You are not due extra bonus miles just because you arrived in LAS 1.5 hours late, and you are certainly not due extra miles just for not being re-booked in full F. It's only a loophole, not an entitlement.
Write a letter to Continental with the necessary details and request the 41 mile EQM adjustment.
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"It's as easy as 1, 2, C" -- Kelly, Married With Children