ALT_MEMPHY is a stubborn thing and your compilation will keep failing, no matter what frequency, because the incorrectly routing pins can not be connected to the internal resources used by ALT_MEMPHY.
Depending on what you expect to do with the board :
- If you want to use other Altera IP you have to correct the PCB
- In the other case you could develop your own phy, together with your own controller, which is a rather big undertaking.
I'm currently in the process of developing my own Phy/Controller combo, as I find the resources used by the HPC II and the ALT_MEMPHY absolutely ridiculous, certainly if you one is using DDR2 at the lower frequencies of 125 and 167 MHz. But for safety (and perhaps sanity) I have made sure the ALT_MEMPHY will work as well.
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