Mine is (card facing me, connectors from right to left)
J0 - 1
J1 - 2
J3 - BT
J2 - 3 (extra cable that was not connected to my original airport card)
BTW: Everything looks good in the Profile as as far as Handoff support is concerned. Preferences look good also. But I still could not get it to work on my 1,1->2,1. I used the Continuity Activation Tool also. Luck.
If you want to swap 1,1 to 2,1, you need to use Mac Pro 2006-2007 firmware tool in os 10.7.5. I had tried the tool in os 10.11.6, and nothing change at all.