The Vref pins in the banks with the DQ signals need to be connected to the midpoint of the 1.8V supply voltage to the SDRAMS, or 0.9V Usually this 0.9V is either derived from the Vtt controller when using DIMMs or made with a 1k/1k resistor divider in the case of single chips.
Also if you drive too many outputs and bidirs in a single IO bank the compiler will also complain. I estimate you will need 4 banks of a 256 BGA or 3 of a 484 BGA device. I'm not sure about the 324 BGA one.
Live IO-check is not complete either, it will only check the number and type of IOs. You may want to instantiate a DDR2 controller together with the Altera-provided test driver to verify proper connection of DQ, DQS and DM pins.