Max Gpio mhz for cyclone II, III, IV ?

See the Cyclone III literature, more specifically the configuration chapter.

Also, triple check your pin assignment with the pin connection guidelines and by compiling a mock up project.

There are many possible mistakes when designing such a board...

If you want to run NIOS or something like that, yes, you should leave extra room the in the configuration ROM. They're cheap, anyway.

Like Daixiwen metioned, the regular LVDS outputs on a Cyclone III aren't no where fast enought for SATA (1.5 Gbps at least).

You'll need either to use a FPGA with transceivers *or* find yourself a cheap PCI to SATA controller chip such as SiI3114.