You've chosen a mod designed by Random Hero, the founder of the board here. And the diagram you link to is on our member wolf's website. So, yes, we can help.
You don't see the Vol and tone controls on wolf's diagram as it shows the "switching module" only. At the bottom of the diagram are two wires, one shown to ground and the other shown as "output". The ground will go to the back of one of the pots (where all grounds will be collected), and the Output will go to the Vol pot.
Earlier in his website, wolf shows this diagram of std Strat V and T wiring:
If you want the std Start arrangement of V and 2 tones, just follow that diagram. The output from the switching diagram would go to the CW lug of the vol pot. The tone pots need to be wired to the mid and neck pickups, respectively, off of the 5-way switch.