Something is wrong about your power supply. Please measure the voltage across the power supply jack to make sure it is really 9V and not 12V.
On the original power supply you were using (the 9V, 1000mA supply), is the jack polarity correct (positive on the sleeve, negative on the tip)?
Generally, all the intermittent issues (of the pedal not working at all, and then not passing signal…etc) are probably related to bad solder joints. It might help if I could see some detailed, in focus, pictures of both sides of your circuit board. Try to bend the pots up some to capture the solder joints under the pots. If i could see the your solder joints and build quality, I could probably offer some better suggestions as to what direction to lean toward in troubleshooting.
-Brach