Is there a 10/100M Ethernet (Fiber/Copper) PHY IP core for Cyclone IV E or Cyclone V

I don't see how the RX PLL for a fibre PHY should be implemented in Cyclone II, perhaps you can tell the name of PHY IP you have used. In any case, there's no Altera (or a competitor's) FPGA that incoprporates the 10/100 MBit ethernet "copper" interface. The only copper interface supported by Altera FPGA on-board hardware so far is a 1000BASE-CX "short haul copper" interface, not compatible with the industry standard 1000BASE-T twisted pair interfaces.