About Stratix4 IO feature

Is the hold time 0ns? I'm guessing not. I don't know why they even give setup/hold times anymore, since PLLs/delay chains allow you to shift to about any setup time you want(but always at the expense of hold).

For 3Gbps, you would need to use the high-speed transceivers. For 1.6Gbps down to approximately 900Mbps, you can use LVDS with DPA. For 900Mbps downto 500MBps, straight LVDS should work. For below 500Mbps, regular I/O using DDR registers should work.

Those are really rough figures off the top-of-my-head, and dependent on I/O standard, board layout, speed grade, the other device being connected to, etc., but hopefully in the right ballpark.