Nios II evaluation board limits

Yes, custom instructions are not board-specific. CIs are bits of HDL that you can attach to the CPU using SOPC Builder. These little hardware circuits are called as macros from your software application, generally replacing a software subroutine. For more info on CIs, check out this document:

custom instruction user guide (http://www.altera.com/literature/ug/ug_nios2_custom_instruction.pdf)

Also, there's an online demo available that will walk you through the steps needed to add a custom instruction to your design. Check it out:

http://www.altera.com/education/demonstrat.../onl-nios2.html (http://www.altera.com/education/demonstrations/online/embedded-processor/onl-nios2.html)