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Yes. Connect all the system peripherals through pipeline bridge (e.g. sysid, jtag, timers, etc). Also fix timing warnings. It is possible to run Nios II @ 133MHz on Cyclone speed grade 8 and ~160MHz on the fastest speed grade. Maybe more, but I've not tested that.
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Thanks for the suggestion Socrates. I am really hopefull that this will get me out of the rut that I have been in for the past several days. However, now I am back to the old problem that keeps showing up whereby the System ID and Timestamp cannot be found.
The system is running at a conservative 50 MHz and Timequest is not complaining about not meeting constraints.
I tried with the Sys_ID component inside and outside the pipeline bridge, but neither work. It was working before I added the pipeline bridge to the Qsys design.
I attached a screen shot of my Qsys design as it stands now.