Is it acceptable to connect multiple unused Stratix II GX positive and negative transceiver signals of the same type through single 10K Ohm pull-up or pull down resistors respectively?

Yes, it is acceptable to connect multiple unused positive REF_CLK pins or unused positive GXB_TX  pins to VCCT_B or VCCR (if tied together with VCCT_B) and multiple unsed positive GXB_RX pins to VCCR through a single 10 kOhm resistor and multiple unused negative REF_CLK or GXB_RX or GXB_TX  pins to GND through a single 10 kOhm resistor.

You must bus the same unused signal type to a single resistor i.e connect multiple unused REF_CLK pins to one 10KOhm resistor, multiple unused GXB_RX pins to one 10KOhm resistor and multiple unused GXB_TX pins to one 10KOhm resistor.