I am happy to tell you that I am using the same board that you have!
Anyway, to deal with old versions you would only open the SOPC Builder and chose to upgrade the design and then continue using your version normally.
Tell me what assignment did you use for the DDR2 pins? I think that you assigned them using the
ep2c70f672 board location while you must use the
original ddr2 core location (Refers to the
reference manual of the board.)
I again recommend to use the standard design which comes with the board documents (<..>\Kits\CycloneII_DSP_Kit-v6.0.1\Examples\NiosII\example_designs\verilog). The design has its correct assignment and any other parametrization.