Alan,
Well to change the output direction you should only have to swap pins 5 and 6 so that the output stage operates as an inverter. However from your description it is not operating as I expected ( I expected the output to go high when the light was shone on the sensor) so I may be wrong on this. Perhaps someone else can explain it to me. Could the IC be damaged?
The other way of changing it is to swap over the sensor and the 10k resistor.
Also it is not really meant to drive a LED, so it might be an idea to increase the LED resistor to 1k which will make your output low lower.
Baz
 
Alan Womack  wrote,
>I need to change my output from being high, dropped low, to being low brought
>high so that the DS1994 iButton will register the over 5v condition as a pulse.

>What changes do I need to make to the circuit for this? The iButton needs to
>see a low signal inorder for the bus to be read by the DS9097U.