Unlikely that you fried anything.
The LEDs are a separate little circuit, and the reason they didn't work with the board removed (I'm betting) is because the ground connection requires the input and output jacks to make contact with the metal inside the enclosure. You could test this theory by putting it back together and seeing if the lights come back on, or by running a jumper wire between the sleeves of the I/O jacks.
Does it pass clean signal in bypass mode? If so, we're looking at the most common problem we see here: light comes on, bypass works, no sound when engaged. Solution: reflowing all your solder joints.
This post has lots of details about that.
For better help, please post photos of your build, making sure they are large and clear enough for us to see details such as the color bands on your resistors. Please include photos of both sides of the circuit board as well as your wiring. If you need help posting the photos, let us know.