The ignition system and lighting system are separate from each other. You can convert the lighting system to dc while leaving the ignition alone.
To use a single phase rectifier with 2 input leads and 2 outputs you will need to go into your stator and disconnect the lighting system ground from the frame and solder in a new ground wire coming out of the stator. You would then connect the two light system wires from the stator to the two yellow wires on the rec/reg. The red output wire will connect to the yellow wire/battery positive for light power. The black wire will connect to the battery negative/ground wire from your led's which can no longer use the frame for ground. You will need to run ground wires for both head light and tail light back to the battery.
Wiring diagram for 1st gen 200x.
85 Kawasaki KLT 160
85 Kawasaki KLT 110
82 ATC 70
2000 Scrambler 500