Hello Michael,
Have you checked the datasheet of the ULPI interface IC? In case of the USB3300 chip included on the TWR-SER2 board, it has the capability of enabling/disabling the internal pull-up/pull-down on both D+ and D- pins. Regarding the software, you could refer to the examples for TWR-K60F120M and TWR-K70F120M boards from Freescale USB Stack v4.1.1 or MQX v4.0.2.
Hope this will be useful for you.
Best regards!
/Carlos