For sure, you need to charge the battery until you sort out the problem. Next you need to test the stator for charging and the Voltage regulator for correct operation. Not a Honda guy, so I'm as useful as **** on a bull, haha
1 thing, I noticed with my Arctic Cat gas models, plowing snow with the winch running all the time, headlights on, and hand warmers cranked, after about 2 hours, my headlights would flicker (low voltage). Charging system couldn't keep up. Tis winter I bought an AC 700 Diesel that has an alternator, like your car! What a radical concept. Never run down the battery now. So, just realize, the little stator on your Honda, may not be able to keep up, if you have a lot of drain. Why Honda chose electric shifting baffles me. I'd check for a draw there.