what you need to pull this off is either a new 3 way switch that is Double Poled, or a dual ganged 500k pot or a concentric plus another cap. your tone control setup is the problem. the thing is you have no way of sharing both pickups on 1 tone control. that is the reason for a dpdt 3way switch or a dual ganged or concentric potentiometer.
the input for the buffer should come directly from the 3 way's output lug. you could get it up and running by doing this and run the tone control output wire directly to one of the red wires of the humbuckers. that is it though, only one of them. i used the bridge in the picture. here is your pic revised to get it up and running.
i would have to see the 3 way dpdt you would use before i could draw you something out, but if you use a dual ganged or concentric 500k then you obviously would need another cap. the other humbucker would be wired identical to first one except the output of the tone control would go to the other red wire on the 3 way.
fyi, i have only seen concentric pots in audio(log) tapers. you may have some luck with a RV4/type J dual ganged 500k on ebay. mouser sells some but the shaft may be too short, it may be worth a try.
to achieve series/parallel AND single coil tap would require an on/on/on dpdt switch for each humbucker. if you wish to have series/parallel an on/on dpdt switch is needed for each humbucker. series/single is the only configuration of the three that can be shared on one switch. if you are interested in the other two, using either switch mentioned, just wire the switch for each pickup like wolfs schematic at dozin.com. wired that way and the on/on/on dpdt gives you all three settings because of the way the switch works and with an on/on dpdt switch will give you series/parallel. it wont work with the wiring you already have, and to be honest you will probably quite happy with the super 2's in single coil. what will get you a ton closer is putting in a middle humbucker, but i am sure you will get there eventually!