Ender 3 under extrusion
OK, I have my Ender 3 back to printing nice looking objects. It turns out at some point since the original bad E-stepper I must have pushed the "load settings" menu item. I set my E steps to 98 from 93. and then did a "save settings". I have no idea why going from 93 to 98.03 increased my extrusion from 40mm to 100mm (trial and error, because the formula said I needed to go to 232.5!).
For those that don't know, the "save settings" stores the current settings in EEPROM. These setting override the factory configuration setting when you reboot. If while you are messing with setting and you lose track of things you can do a "load settings" to get your previous settings back to start again. The "initialize EEPROM" reloads the stored configuration settings including the settings that you saved. 
More intelligent explanation here: