Leave it on the charger for a few hours, and it sounds like you have done that. Once you have the bike put together and it runs, then go for a few short rides, followed by full recharges of several hours after each ride. Just a couple low depth of discharge cycles helps the new battery get balanced better. By the 4th ride, you should be able to go for as long a ride as you like.
The charger should show red while charging, green when done, but leave it on the charger longer. If it needs any balancing, the bms will handle that, but it will take hours, and the charger light will go red briefly from time to time.
I have never had a problem from leaving the bike on the charger overnight regularly. The bms is supposed to prevent overcharge, and undercharge can lead to problems like getting out of balance.
Re the voltmeter. so many ways to use one wrong, including just not geting good contact at the probes. If you are seeing about 56v when you connect the voltmeter to the battery discharge terminals, you are about where it should be. Some lifepo4 will come off the charger higher, but about 55-56v is the fully charged voltage for 48v lifepo4. 48v is about completely discharged.
Regarding the charger lights. Green only is either charged, or the plug is broken or disconnected from the battery. So what the lights look like when you plug in the charger not connected to the battery, is what "charged" should look like. Sometimes the green light partialy leaks over to the red spot making both look lit. Both may be lit fully when it is charging a battery, then the red light goes out, or just gets dimmer when it's done.
Some of the cheaper chargers can be confusing what the lights mean, but you should see some change when your battery is charging vs when it's done.
THE LIPO RULES. NEVER ABOVE 4.3V NEVER BELOW 2.7V DON'T PUNCTURE
Ideal charging /discharging range for Lipo, 3.65v minimum 4.1v maximum
See battery technology section, FAQ thread at the top of the page for lipo noob info.