Revisiting this again.
After sorting through the harness I got with all the parts I bought I notice the regulator/rectifier will not mount back on the subframe like in the pics above. It will have to be mounted next to the ignition coil where the old AC only regulator mounted unless I would to add a bunch of wire and do some splicing. As you can see from my pic, the wiring doe not appear to be hacked up and it has the ground that bolts to the regulator. This all came from a 2013 bike so I'm kind of at a loss here.
Should I extend the regulator back to where it is supposed to be or will it be fine by the coil?