So, to clarify,
If you have a 48v battery, you don't have a 250 watt motor. Generally the smallest fixed current is 10 amps, so that gives you roughly a 500 watt motor.
Yes, all batteries are charged over their nominal rating. LiFePo4 even more so. The charger has the charging voltage listed on it, that is what you have hot off the charger.
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shabydog, voltage = speed. current = power (torque). I don't know the specs on your motor, but 48v usually gives a pretty strong/fast motor. You could use a 52v battery, but that is going to give you about 8% more speed. Not a lot.
If you want more power (for hill climbing or acceleration) you can get a controller with more current (or just solder the shunt some), or a programmable controller. The problem of course is that if you add more current you add more heat. That means it is easier for things to start melting. Typically you may be able to get away with 20-30% more current if you don't have a lot of hills. Going full power up a hill (or full power anything) for long at LESS than 50% of the motor's cruising speed on flat land is when you start to get into the danger zone.