I have wired the timer switch to a 2 speed toggle switch and I get nothing but high speed on a brand new Marathon motor..

Is this a two-speed timer or a single-speed? You'd need a two-speed timer and a two-speed toggle switch to accomplish that. Are you swapping an old motor for the exact same model or is this a new installation? Post the motor's, timer's and the switch's part numbers, I'd like to take a look at the wiring diagram before sending you in a wrong direction.  Does it operate as expected from the toggle switch alone? 
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I wired to schematics that came with the fan motor, neutral to neutral, the black speed to one side and the other black to the other side and then grounded.
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