Custom ip: can't see IRQ number in system.h

Which version of the tools are you using? I remember running into this in the early days of Qsys but I thought these issues were fixed. -1 represents a disconnected interrupt number so assuming you have connected the interrupt sender to the receiver (Nios II) I would have expecting the interrupt number to be populated in system.h instead of -1. Often when I ran into this issue it was when I fed the interrupt through a bridge connection (often to drive it up or down the Qsys system heirarchy). So if you describe the connectivity more I might have a workaround that will work for your system.