On the new computer I am building the system fan has a 2 pin female connection. No problem for the motherboard but I want to connect it to a fan control with 3 pins. Can I just fit the 2 pins in to match the red and black wires or do I need an adapter?

just fit the pins to the locations of the old red and black 3 wire. if it spins and you dont see smoke youre in good shape.

Could I put a new 3 pin fan on (if I can find one to fit). It is a 40mm x 10mm for the chipset of an Epox 9NPA+ Ultra board. Well?????????

Just use any 3 pin fan with the same size and power requirements. If you want real control, you will need the 3rd pin.

For 2 pin fans, the red/yellow cable is 12V (VCC) and the black one is GND. Review the male connector, if VCC and GND are successive, you can connect with no adapter (well, depending on the female connector form and size).