A couple answers...
1. you can download the Nios Ii eval from this forum (look at the download section).
2. The error/message about the cable is to warn you that the cable you are usign MIGHT give some errors.
We found a problem (I'll paste from the errata at the bottom of this post (it's long)).
NOTE: we use byteBlaster MV and II cables for our testing, they may not be the latest and greatest, but we use them constantly. The flash programmer will stress the cable such that you really want to use the revB USB cable, or a modified ByteBlaster (II or MV).
3. I'm not sure about the design problem, but my guess would be that the Microtronix board doesn't have many things that are on the Nios board. The boards would have to have all the things the design requies and the pinoput would need to be the same for the design to work.
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Download Cables:
You must use a supported download cable when downloading,
debugging, or communicating with Nios II systems over JTAG.
Using the USB Blaster Rev A, ByteBlaster, ByteBlaster MV,
ByteBlaster II, and MasterBlaster cables may cause intermittent
JTAG communication failures.
The modes of failure are:
* Debugging Failure with the Nios II IDE - Debug session
terminates with JTAG I/O error
* Nios II JTAG UART Failure - Invalid characters transmitted
and received via Nios II Terminal
* Device Configuration Failure - Device configuration fails
with an error message from the Quartus II Programmer
* SignalTap Failure - SignalTap session terminates with JTAG
communication error
If you receive the following message while using the Nios II Terminal,
the tools could not verify whether you are using a supported cable.
nios2-terminal: Warning: Unable to verify whether your download cable is supported for Nios II systems.
nios2-terminal: If you use an unsupported cable, you may experience intermittent JTAG communication failures.
nios2-terminal: Please refer to the file errata.txt included in the Nios II development kit documents directory for
nios2-terminal: information on how to update your system.
In general, the above message will only occur if you have
re-installed Quartus II 4.0 SP1 after you installed Nios II
version 1.0. Re-installing Nios II will allow your system to
detect if your cable is supported. The warning message will
occur each time Nios II Terminal is started until you re-install
Nios II.
If you receive the following message from Nios II Terminal, you
are not using a supported download cable. The warning message will
occur each time Nios II Terminal is started and an unsupported cable
is detected.
nios2-terminal: Warning: The JTAG cable you are using is not supported for Nios II systems.
nios2-terminal: You may experience intermittent JTAG communication failures with this cable.
nios2-terminal: Please use a USB Blaster revision B cable or another supported cable.
nios2-terminal: Please refer to the file errata.txt included in the Nios II development kit documents directory for more information.
The supported cables for downloading, debugging, or communicating
with Nios II systems are:
* USB Blaster Revision B or later
Revision B cables are clearly labeled as Revision B.
(Revision A cables have no revision label.)
* Please contact Altera for additional information
about supported cables.