Best surgical way to archive, wipe and clean install Catalina on a 2017 MacBook Pro Long story short. 

My MacBookPro has become bloated with files that I either can't trace back to originals or have no real memory of three years later. It’s got a 2tb SSD and i am constantly running out of space - yet fearful or deleting system files

(btw feel free to edit if I am not asking this in the most effective way.)

I am getting constant errors in console such as

&lt;private&gt; worker reports error after processing object &lt;private&gt;, error: Error Domain=com.apple.photos.error Code=47001


My question, is there a way to safely back up either via Time Machine or via individual files the things I would like to save i.e. photos documents, movies, Snippets of code, BBedit files etc. And then reinstall them without potential he re-infecting my machine with malware which I believe there to be present although I have not been able to track it down.

Model Name:    MacBook Pro
 Model Identifier:  MacBookPro14,3
Processor Name: Quad-Core Intel Core i7
Processor Speed:    3.1 GHz
Number of Processors:   1
Total Number of Cores:  4
L2 Cache (perCore): 256 KB
L3 Cache:   8 MB
Hyper-Threading Technology: Enabled 
Memory: 16 GB
Boot ROM Version:   ****
If you believe that macOS has been infected by malware, then you can try reinstalling macOS from macOS Recovery without losing personal data and settings.

If you believe that malware has infected your personal files, then I would recommend backing up necessary personal files to your external hard drive by copying and pasting them. Doing a Time Machine back up will bring your problems along with you because it backs up every single thing. 

After you have your files, boot into macOS Recovery (reboot then Command + R). From there, go to Disk Utility and Erase Macintosh HD (and Macintosh HD - Data on Catalina). If you are on Catalina, then you will get an error when attempting to erase the contents of Macintosh HD (system files). To fix this, go to Terminal and type 'rm -rf /Volumes/Macintosh\ HD'. Then follow through with the erase. If you want to make sure that nothing on the disk exists after the erase, then choose Security Options and increase as needed. This will erase everything. Then, use macOS Recovery to reinstall macOS.

Good luck!