It sounds like the bad VR could have caused damage to the EHC module. You could use a wiring diagram for your "07" K9 to get going. I sent you a PM (private message). If the EHC did get trashed you can either buy a replacement BDM EHC or replace it with either a Wire Plus module kit or inquire at BDM for delivery on their new EHC replacement kit due out soon.
There was a factory service bulletin on the VR. Newer ones are identified by date or somehow, can't recall now. Your "07" should be okay. Check the Technical forum service bulletins.
Not sure if the K9 has a second branch fuse somewhere. I only see the main 40A fuse or CBrkr, but you say you do get a rear light on so that fuse sounds okay.
Make sure your battery terminal wire crimps are all crimped tight on the wires. Mine worked loose and caused weird EHC like problems. Weird LED light display, engine dies, no nothing when key on.
The Wire Plus kit has been used alot here and works well. Would be my first choice if you need to go that route. It does involve some wire harness cutting and changing bike harness to new WP module connectors.
Wire Plus Module here:
Wire-Plus Big Dog EHC Module WP-374 2004-2010 Models - Low Down Chop Shop
Wire Plus Module installation instructions:
http://www.bigdogbiker.com/forums/how/7946-how-wire-plus-hand-control-module-ehc-removal.html