1. Check all connections that go to ground or power. Use a multimeter to verify continuity and proper voltages are present.
2. Check all of your connections, especially making sure that everything is supposed to go to ground does indeed to go ground.
3. Make sure that all points that are supposed to receive power really are getting power by looking at the connections and by measuring with a voltmeter. Connect the black lead of the voltmeter to ground of your circuit and touch the connection with the red lead of the voltmeter.
4. If you have changed a transistor or IC, double-check the orientation of the transistor or IC, make sure that the transistor or IC has the right pins in the right places.
5. Check the orientation of any electrolytic capacitors.
6. Check your resistor values throughout your circuit. It is easy to accidentally use a 470k resistor instead of a 4.7k (for example) and this could easily make a circuit not work correctly or at all.
7. With the circuit powered, measure the voltage at the battery terminal and make sure there is ~9 volts. If there are zero volts, it's possible you have a short in the circuit.
8. Very gently twist the circuit board and/or move the wiring connected to it to see if you have bad solder connections. Sometimes the circuit will spring to life because of a bad solder joint and this can help to show if you do or not.
9. If you are testing the board in the enclosure and it worked while it was out of the enclosure, look for any place the enclosure or a pot or stray wire might be touching the board or a wire and grounding out the circuit.
10. Make sure when you put the pedal back together that the Pots lugs do not touch other pots or the case.
11. If you are still having problems at this point, make an Audio Probe (see below) and trace through the circuit. You should have one anyway if you are building and modifying pedals. Build it, use it, and it will make things so much easier to fix.