The MUFF’N has two clipping stages. Each will create a decrease in signal level. If the first one is actvated by SW1 and the second one by SW2, there will be a second decrease in level.
The amount of decrease is determined by the forward voltage of the diodes. You can increase the level by using diodes with higher Vf. LEDs would have the least amount of level loss.
If you still have excessive loss, then check for bad connections in that portion of the circuit. Resolder.