Hello janhendrik,
Take a look at sheet three of the Cyclone DK schematic. “pld_CLKOUT” is used to drive the clock buffer (49FCT3805). The buffered “pld_CLKOUT” is used as the feedback for the second PLL to drive the clock of the SDRAM. So if you change the frequency of “pld_CLKOUT” you will also change the frequency of the SDRAM. If you need a 40 Mhz clock at a proto-header you can change the frequency of the system in every stage or you put a 40 Mhz clock source on your expansion port (this will create a asynchronous system).
Bye,
niosIIuser