For Percentage Not Showing Correctly:
# Discharge the battery(by using the phone without it being plugged in) until the phone automatically shuts off.
# Charge the battery until 2 hours after it reaches 100%. Make sure your phone is off while it is charging(About 3 minutes after your phone is plugged in, the phone will turn on and you will need to turn it off).
# Turn the phone back on and make sure the percentage meter works correctly.
For Non-Genuine Battery Message: This is a message by Apple that pops up whenever someone that is not Apple-Certified replaces a battery. This message will show up whether you use a genuine Apple battery or not. The only way to get around this is to use an iPhone Battery Serial Number Reprogrammer.