NIOS II Stratix board pin map

To help with debug can you ensure that the SysID peripheral is in your system (make sure your hardware and software are in sync). Also I think Kerri meant "qsf" file which you will see a lot of pin assignments. I would just copy the ones you really need and leave the rest unassigned. Another thing is, you should make sure that all unused I/O are tri-stated (it's in the Device&Pin settings). That was you don't have stray I/O being assigned where you don't want them to be (like a pin connected directly to ground for example).

If you have LEDs available and routed just like in the standard design, I recommend that you use "Hello-led" to see if the design is alive at least (that way you have minimal reliance on the JTAG uart). If that looks fine then work from there.

Good-luck