A couple of things...
1. I wouldn't really expect to see much light from the LEDs - certainly not as bright as your picture shows. For them both to be lit at the same time suggests one is round the wrong way.
2. Switching power with the bypass stomp-switch is not a good idea. Particularly in the middle of a song.
3. A plastic box means you'll pick up radio stations, microwaves and WiFi.
4. Your switching scheme means the circuit is constantly sucking at your guitar signal.
If you can't get hold of a 3PDT switch, check out R.G.'s Millennium switching system (at the GeoFEX link above). And use one of the common schemes for wiring jacks and batteries so that power is switched on when you insert your guitar lead. I use the ones at
Tonepad all the time.