Hi Emre,
I just uploaded a new version of the IPs that don't have input frequency parameters, so they should work with whatever input frequency you give them. I think the ext_spi_clk still needs an input frequency of <50MHz to work though.
You can create new clocks by double clicking the MIG IP block. Click "Next" until you see "Select additional clocks". Check the box and choose the clocks that you need. Then click Next Next Next Next,Validate, OK, Next, Next Next Accept, Next, Finish. It's a bit of a pain, but that's the MIG.
Hope this helps!