Thank you Edouard for your thoughtful and detailed reply to some many issues.
I thought I would post some updates on several of the issues in my original post for the reference purposes in any case anyone else experiences similar situations.
1. fan in base is very noisy
This issue seemed to be related to strings of filament inside the Base, artifacts of the 3D printing from the extreme overhang inside this object.
I was able to substantially reduce noise by cutting away the strings and artifacts that I found during a teardown of the Base following the YouTube videos in the Assembly Manual.
2. “gear grinding” during calibration
3. lurching (non-smooth) movement on some axises
6. double calibration necessary to issue commands without receiving errors
These issues seem to have been resolved for the most part after the work that I have done in rebuilding Axis 2 and Axis 3. Please refer to additional detail of this work in my other posts in this section of the forum (“Niryo One calibration issues” and “plastic shavings under shoulder and motor for joint 2”).