Often when bars are changed you lose the ground for the bars. Painted bars prevent contact between the switch housings and bars as well as bars to risers.
The horn and starter button use the bars for ground.
You say the bike cranks fine so you grounds should be ok. When you had the right side housing off you may have pinched the red/white wires for the engine stop switch. This might be partially shorting to ground. This could weaken the power to the coil, causing weak spark.
Other than that there is very little effect changing the bars could have.
Leo