It's a pretty plain system right now. Everything is contained within the FPGA. So their is logic added to do communication across the custom hardware interface, and I added a hardware divider that I created (since that core doesn't have one). The divider on it's own has an Fmax of 150, and after the timing analysis is complete is not part of any critical paths when used by the NIOS. The critical paths are all in the ALU, and I'm finding the logic in the messages having names like MUL, pipeline, shift (if I remember correctly, I'm re-building right now so that I can get the exact names). Also to rule out my divider, I've put it into the 'f' core and turned off the Altera provided one, and my timing and processing performance is not affected at all.
When I use the 'f' core then the NIOS is simply restricted in fmax by some of my surrounding logic (and the fmax is what I'm expecting). So I have a perfectly fine system using the 'f' core, but it's a bit overkill for what I need, and I'm able to get almost identical performance out of the 's' core due to my design. But I'm not going to trust my design running on the 's' core until that fmax is at least 10Mhz higher since this design will be dropped into a much larger design.
Is it possible that the ALU has problems targetting the 1S10ES device? (NIOS development board).
Thank-you for you're help and any additional insight you may have.
*Edit* I've been using the minimal debug capabilities to download code. I'm starting a build without it to see what happens.