I used the built in configuration options on my Ender 3 Pro rather than doing it through the computer. Having the extruder at the default 93 resulted in less than 100mm of travel. I don't recall what the amount was, but I simply took 93 * 100 and divided that by the amount that was actually extruded. That gave me a value of 97.2 for the new E value. After doing that, it hit 100mm pretty much exactly.

all3dp has a good guide. https://all3dp.com/2/ender-3-calibra...-your-ender-3/