If you have the relay under the hood connected, bypassing the one on the pedal will work. If you bypass the one under the hood it doesn't care what the switch on the pedal is doing.
Below is a picture of the connector under the hood after the large blue relay has been bypassed. The wires going to the left tie into the chassis and are untouched. I found a mating connector with the same wire colors and gauge. To the right the b/w and b/y wires are crimped together and heat shrink covers the end. Makes it easily removable as an extra layer of security if you park the car somewhere.
