I just recently bought a gigabyte motherboard and I hooked everything up but, since the case is an old sony vaio computer I don't know how to connect the front panel wires. They are different in position on the connection and once I plug them into my gigabyte motherboard the computer does not start up. Do I need to rewire them to the connector?
Well the gigabyte mobo instruction book will have a pin out of the motherboard connector (or it may be printed on the board itself). For the case connector, you'd have to look for a sony support guide - it's unlikely that they publicly release that information since they want to keep you buying replacement parts from them.
How much experience do you have in re-wiring?
Also, did you check the specs on the OEM PSU? Most of them aren't very good...