All of those issues you mentioned are run off the small 12 volt battery and have nothing to do with the drive battery. Did you reprogram the charger for the lithium battery? I would check your 12 volt system. Possibly you have lost your 12 volt ground. Good luck!
You really want to use an automotive or motorcycle battery tester to test your 12 V battery, and not just a multimeter. The automototive tester will apply a load to the battery and measure the voltage while the battery is discharging through the load.