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I know that the mode should be the same, with a ping should it work?
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It MUST, not it should. Please check this point; if the NICs you are using allow it, force a fixed mode, rather than auto negotiation.
When it works, ping and everything else will work, like you connected the two Ethernet cables together.
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About the clocks, if I'm only wiring from one connector to the other, should I take care about the synchronization if I'm only connecting one input with one output??
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The PHY has separate tx and rx clocks outputs. Then simply wiring input and outputs may not be correct.
You'd better use some registers to sample phy rx* signals with rx_clk and then drive tx* signals synchronized to tx_clk.
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I thought that the mdio is preconfigured in this kit and is not needed to be configured for this purpose, am I wrong?? if yes, I thought that there was an ipcore from altera for this configuration but I do't find it, do I need nios? because I'd to avoid its use
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You are right. I took a look to DE2-112 manual and I saw there simply a jumper to select RGMII or MII. Set it according to your NIC mode.
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