2009 Savage, 1900 miles.  No electrical modifications other than upgrading to louder horn.  Intermittently, L turn signal doesn't work.  When L turn signal switched on, all lights (turn signals, low beam, brake light) flash.  When this happens, I feel bike will shut off on me while riding (been vigilant to make sure I'm not hitting kill switch or kick stand switch).  Things I've done to trouble shoot:

-  cleaned the turn signal housing and connectors - all clean and good
- Checked bulbs - all good
-  replaced flash relay
- tested regulator/rectifier and alternator - working fine
- Got new battery.
- checked wiring under seat, nothing looks compromised (haven't looked under tank yet)

At this point given signs, I'm leaning towards bike is shorting somewhere,   Lastly, I feel the seat gets hot when I'm experiencing these problems too.  Any help would be greatly appreciated as I love this bike.  Bought a new Yamaha MT-07, but prefer riding my Savage around town.  She's soooo much fun.

The lights you named all share black and white ground wires ,Follow Vercy's advise , there 's a hot wire touching one of the ground wires (short) and is most likely to be inside the head light housing . you might try unplugging the new horn ,but I'm not sure that will help,  even if you hooked the wires up backward.