[Water Warrior 2]

First off you may need to give the bike a dose of Sea Foam. Backfiring(actually afterfiring out the exhuast) may be a sign of lean running with a Cali spec bike. Also check for an air leak at the rubber boots on the carb. Both intake and discharge sides.
Question, did you do an oil change? I would recommend fresh oil. And the bike isn't broke in yet either so you have a tight engine needing some break-in time to smoothen things out. Use regular gas, no high octane is needed and is just a waste of hard earned $$. Check your tire pressures too. I used to set Lynda's GZ for 2 up riding. Slightly higher in the rear tire for 2 up. On long rides I would exceed the manual #'s by 2 or 3 PSI for better tire wear and mileage.
Oh yeah, before you put the new battery in service make sure you fully charge it up or it's service life will be shortened.
Ah, I see Alantf is way ahead of me.