AFAIK, if you leave your device to charge overnight it charges the phone to 100% and then stops charging (the battery would be damaged if it was "overcharged"). Then, when some threshold (~90%) is reached it starts drawing current again and charges it back to 100% when it is cut off again. The reason you see 93% (or whatever) in the morning is because it has reached 100% earlier and hasn't started to charge again. I don't think it has a lot to do with data connections.

It might be possible to calculate the charging time required for 100% at a given time and write a script that would control an external power source to turn on and charge the device for just the right time, but I very much doubt it would be worth the trouble.