Your response has given me what I needed so I could point my research in the right direction, I didn't realize that the entire analog section should be isolated until I researched it further (as a direct result of your response and advice!).
Thank you so much for that!!
You are right, the low pass filter is not package specific, as it turns out I simply missed the part concerning the low pass filter and analog ground plane layout, I must have been really tired and it just didn't register in my brain. 
I found that section (page 258 I think) and it makes sense to use the filter as long as I use a proper isolated ground plane around all analog pins, the filter without the dedicated ground plane probably wouldn't help much.
Now it makes more sense about the .1uf caps since one of them is isolated with the analog ground plane.
After I complete the PCB, I plan to run some tests with a scope for noise and accuracy. I ran some tests today on a Pro Mini and it's not very good as far as noise on the analog pins is concerned so hopefully adding the filter and isolating the area around the analog pins should show a reasonable improvement.
If you like, I can post the results here when I get it done (I can take a few photos of my scope and post some numbers to go along with it).
Obviously I will have to redraw that part of the schematic, the ground pin nearest to the AREF pin is connected to the analog ground plane (along with the .1uf cap from AREF to that same ground plane).
That ground plane should not be connected in any way to the chassis or battery ground since it's actually connected internally (inside of the Atmega 328 processor).
I have attached a screen shot showing the suggested low pass filter and analog ground plane along with what I did in my PCB layout, obviously I will have to make some changes!!
The caps are fairly close to the processor now but they should be closer (like in the example you posted), there's no dedicated analog ground plane at all in my PCB layout!!
It's worth making the PCB a few millimeters larger to get a more stable and more accurate analog reading from the shunt resistor/amplifier IC, I can always find a suitable enclosure, in fact I may have one 3D printed (I can easily model one in Fusion 360).
Actually, The reason I ran the traces the way I did was because of my observations of other Arduino Pro Mini boards (both the genuine and clone versions). I have attached another screen shot showing the layout of one of the clones and it's not too far off from what I did to my PCB layout (not much different from the genuine board either).
I can only imagine that the traces under the processor look just as nesty as it does on the bottom of the board!
I have also attached a screen shot of another portion of my PCB that shows how I normally treat various ranking planes.
I've already done some testing at the output of the on-board switching regulator (with my scope) and I wound up adding a 47uf cap to make the output a little smoother, I had to experiment by using different values until the ripple was just under 30mV, too much capacitance isn't a good thing in my experience and I'm sure you are aware of that fact as well.
The 6 amp buck converter was already filtered properly since it's a POL module.
I used a 6 amp buck converter along with a 7 amp photoMOS SSR, I'm running slightly more than 3 amps through them but I like things to run as cool as possible.
I knew that the header pins for bootloader and programming weren't in a specific order and I did that because I usually use single Dupont connectors rather than a solid 6 pin connector, I use ribbon cables most of the time but the order didn't seem to be that important to me, having said that, it probably would be better to put them in order while keeping in mind that the FTDI Tx pin goes to the board's RX pin (same thing for the Rx pin), I've heard of people connecting those backwards and then have a hard time figuring out why their board won't program.
I can't tell you enough how much I appreciate your help!!!
PLEASE feel free to let me know if you think I've missed something or if you think I'm still not getting this right!!
Respectfully,
Joe