The three-way selector is a good idea. A Freeway switch might have been even more clever. (There is enough space for one under the control plate.) Do you still have the Bass Cut slider switch in circuit?
The slider switch simply diverts some low frequencies to ground via the capacitor. Connect it to the output of the selector switch. Alternatively, rejig the switch for something more useful such as phase reversal or series/parallel.

The diagram that you have posted is for a conventional single coil Jaguar. I would expect several elements of the HH Jaguar circuit to deviate from the vintage norm.
It seems to me that, according to the SD schematic, the capacitor on the Bass Cut switch is always in circuit. Just that, in the "off" position, the cap is in parallel with the connection between the internal contacts of the slider switch.
I have a 50th Anniversary Jaguar as well as the HH discussed here, and the circuits are the same. They are also the same as the 62 AVRI Diagram on Fender's site. However the SD diagram here is not 100% the same as those models, (but it may be correct for an actual vintage model.) On the guitars I have, both upper and lower tone caps are .01mfd. Also the SD Diagram does not have the 56k resistor that goes between the right and middle terminals of the lower tone pot.
This is correct.
---------------------------
To the OP: If you have it wired as in the diagram, with the toggle wired to one side of the capacitor and the other side of the cap goes to the tone/vol controls, and the bass cut switch shuts the guitar off, you may have an open capacitor. You can try replacing the capacitor, or just use it as a kill switch!
Also note that connecting the toggle to the volume control as you mentioned, rather than the tone control, you have slightly modified the tone circuit, because it's different on a Jaguar than on most guitars. I do not know if doing that makes any noticeable difference in the sound though.
my tone control doesn't really have a lot of travel. from 10-2 the sound is the same. it's only when I roll it all the way down that the guitar goes dark.
That is a 1Meg pot for you. Expensive ones behave the same way only, maybe, the transition is a little smoother.
my tone control doesn't really have a lot of travel. from 10-2 the sound is the same. it's only when I roll it all the way down that the guitar goes dark.

crap i wish i would have seen this before I threw out the old 2 way switch.I went back and read what you said when you posted the diagram and now I'm not sure I understand exactly what you did. Just to make sure we're on the same page, here is how I would suggest you wire it. This should be just like stock, but with the toggle replacing the two slide switches:
View attachment 44770
Glenn. In August, you posted that you were going to remove the two Dimarzio humbuckers in the black HH Jaguar. What pickups are in it now?
This is awesome, I plan on modding my own Jag Blacktop. Where did you get the Replacement pick guard from? And have you not replaced your bridge? I had problems where the saddles would fall out of mine and had to replace it.
The stock fender humbuckers, surprisingly. They sound great through my Vox.
In my opinion, this is a backward step. You have undone some good work so as not to show up your bandmates' cruddy instruments. It would be better if they had made upgrades to bring them up to the standard of your Jaguar when it had Dimarzio pickups.