The second/lower of the true-buypass pictures is exactly the one you need to follow: Notice how it connects the circuit board input to ground when the circuit is bypassed.

On the picture of your smallstone guts, the circuitboard input is just off-centre of the board and currently connected by the black wire to the bottom left lug on the footswitch. This gives you true bypass switching, but without the input being grounded (i.e. it’s the same as the TOP picture of the two true-bypass schematics you posted). Just rearrange the connections so it ressembles the second picture. The white wire that emerges from the circuit board immediately next to the input wire and connects to the lug opposite the black input wire is the effect output. The red wire on the switch is the pedal input, and the white wire opposite that on the switch is the pedal output.

Hope this helps…