Hi,
My apologies for not answering earlier. I didn't know of the existence of this mini-forum and did not receive any notifications for new posts!
You two technically already presented your project, but I thought I'd answer in case others have the same problem. The error you were receiving occurs when quartus does not know how to assign the names in your top-level VHDL file to physical pins on the board. Technically you should not have this if you run the pin_assignment_DE1_soc.tcl TCL script mentionned by Samuel. This script is automatically executed if you construct your linux system using the script I provided.
Note that you should also COMMENT OUT all pins that you don't use in your top-level file and only keep those that are connected to an element in your system. I suspect this is the issue you were having.