Large stones, more eggs or capped water bottle will all add thermal mass. Thermal mass is by itself inert, it doesn't do anything as in it wont raise temp. What it does do is hold temperature. By holding temperature you make the air temp in incubator more stable. As for eggs internal temp your looking for 99.5F. A range of 99 to 100 is perfect but obviously 99,5 is best. Your right in thinking the top of egg and bottom of egg is a high and low and it's the average that the inside of egg temp will be. People usually can't measure the temp under the egg so rule of thumb for still air incubators is 101.5F at top of egg and in doing that your ensuring the inside is right temp. That number is based on eggs being upright in turner. If on side then that's a smaller space and 100.5-101 F is more likely a better number.
The deal is there are so many variables, once in realm of homemade incubators even more so. But something as simple as the thermometer is a massive variable. We all aren't using the exact one. Most people don't even calibrate them. So your most important tool in incubating is suddenly suspect. I use an oral thermometer. Cheap and the most accurate device you'll find anywhere near the price point. I've read of $30 dollar Brinsea thermometers being off. Honestly, unless you purchase a $100 lab thermometer just stick with what you have or use an oral thermometer from medicine cabinet or purchase one for $6 at wally world. When using a thermometer keep notes. See what day the birds hatch. If they all hatch a day early the thermometer is reading lower than actual temp, a day late the thermometer is high. Measure temp in the same place all the time. By the end of a hatch you know what temp and where to measure it for your incubator with that thermometer. An off reading thermometer isn't useless it's merely unique, where you measure temp is unique and if you average temp or any other little thing is unique. Do it all the same all the time and adjust what temp your going for by how the hatch was. That dials you in. If birds are piping day 19 and hatching day 20 you'd do everything the same and lower temp by 0.5-1.0 F the next hatch. Of course it's important you measure day 21 correctly. If you set on a Sunday then day 21 is on a Sunday.