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The e of 99.68 seems to print ok on the small prints. If i do a test extrude at this setting I only get about 40 of 50 mm
There is a guide to calibrate e-steps ( and stepper current too ). Both will probably help you improve extrusion quality.
PID tuning can be done once and then store the values in Eeprom. No need to repeat it any time soon.
In Marlin Firmware you can add the U1 parameter to apply the PID results to current settings upon completion.