Upgrading to larger wheels will kill your mileage because of the increased unsprung weight (more metal & more rubber) and the increased rolling resistance (wider footprint).
There is a built in volume to the fuel tank to allow for expansion. If you fill-up using your slow/rock'em/sock'em method and fill until you see it at the top, you have not left enough room for heat related fuel expansion.
Now do this on a HOT day and then let it sit in the sun you are asking for trouble. Liquids are not compressable at all. That is why any time you see a bottle of liquid there is always a space for expansion.
Pumping gasoline stored underground that is cool into your vehicle your way does not leave any room to expand. It may take a while before something in the system weakens from the repeated expansion stressors but someday something will give somewhere--like a gasket or a weld seam, maybe split the fuel line or rupture the fuel filter. Can't say because I am not an engineer but I've taken several physics courses and I have slept at numerous Holiday Inn Express motels!
As far as the manual calculation, it's the average of many fillups that will give you a truer fiqure. Years back they didn't just take one person's temperature and call that normal...they did thousands and at different times of the day to come up with 98.6.
The recommended procedure is to fill at same station, same pump, (if you are super anal--same time of day) allow 3 click-offs and stop. Record your volume and miles, reset and take off. After doing this for several tankfuls and you will begin to see a more accurate average value develop. Want take it a step further? Also record driving conitions with each fillup...all city, mixed and mostly highway. If you group your averages under these headings you can then see the 3 different trends emerge.
Cheers.