FlipFlop outputs half voltage SN74HC74D
Most likely your output is oscillating between 0 and 5 volts to cause an average voltage reading of 2.5 volts. The long leads you have to your switch (?) in your diagram are probably picking up enough noise to cause the oscillation. Try tying a 10k ohm resistor between pin 3 and ground right on your circuit board. 

In general, you should tie together all other unused inputs and connect these to a 10k resistor to ground to keep noise out of the circuit.