Battery backup system and analog reference voltage

Hello all, this is my first post but I am trying to learn as much as possible for a project that I just got some parts in for.

I am working on a datalogging device that will read the value from a load cell and record it to an SD card to be read later and inputted into excel. I am pretty sure that I have all of the physical aspect down, and I recognize that there will be some pretty fair inaccuracies because I am only using one load cell and I am limited to the 10 bit resolution of the Arduino Uno's ADC.

What I am working on now is making sure that the battery backup system is working properly, and I believe that everything on the battery's side is working quite well, it is charging, and it is capable of outputting a well regulated 5V (I measured it to be 5.08V). I am running into a problem with the delivery of that voltage to the Arduino. I have been using the Vin and Gnd pins, but the 5v pin only outputs 4.18v by my measurements, which I think could really skew the values that are read from the load cell, since it is expecting 5v.

I think that my options at this point, if I want to compensate for this difference, are to either supply the power from the battery directly to the 5v pin, or I could pull the Vin pin to the ARef and compensate for that in the coding.

I am not familiar with either of these options, so any and all input would be greatly appreciated. If any more information would help you guys out, I would be happy to provide it, feel free to ask. Thanks in advance for your help.

The voltage drop is probably due to the regulator .

you should check the hardware schematic here - http://arduino.cc/en/Main/ArduinoBoardUno -
to see where to connect 5 V to skip the regulator.

As of now I am connecting the battery power that is regulated to 5v directly to the 5v pin on the arduino. It seems to be working well, nothing is heating up, no puffs of smoke, etc. I think this will work well enough for my purposes.