I designed PCB with Spartan 6 FPGA and my plan is to stack this board with other board having AD or DA converter (like AD9744). I was wondering how fast data rates are possible with pin headers like this: https://www.pololu.com/catalog/product/965 .(and female connectors matching it)
I know there is no simple answer, it depends on line impedances, connector quality, driver and receiver properties and so on. But I imagine someone with more experience can say is 50Msps, 100Msps or 200Msps I can use to drive DA converter?
200 MSPS isn't a problem with 0.1" headers as such, but for the present development board, single ended IO without sufficient ground connections will result in poor signal quality.
What you need to do is to "slow-down" the drivers of your digital signals. In other words, if you can, set the rise/fall times of your drivers to a maximal value for your digital bitrate. If possible, use differential signaling instead of single ended ones.