I'm not familiar with the model of your bike, but unless the headlight/brake lights are DC only, get rid of your battery and rectifier all together.
A rectifier simply turns AC into DC voltage.
The only problem is, you're going to need to install 12v bulbs. The battery acts as a voltage regulator and prevents bulbs from blowing. Without it, your voltage will likely spike above 6v and fry some bulbs up.
Split your yellow wire to head and tail light, and run wires BACK for your grounds to the main ground. I have found that Hondas NEED the ground wire running back to offer more resistance to the circuit compared to light mounted grounds, to prevent the blowing of bulbs when you remove the battery.
Whereever the battery currently is in the circuit, you can just jumper it off and remove it as well as the rectifier.
Hope this helps!