Computer Slow Down Conflict in Mojave? Copying to usb very slow, and more...

Please download and run Etrecheck  It is a diagnostic tool that's very useful to us in finding problems. Also it will give us further specs on your Mac. After it runs post the log file here. It will contain no personal information. Allowing full drive access will improve the quality of the report.

To post the log file click on share report and use the Page icon in your reply window.

Download and run the free version of Find Any File to search for any files with the application's name  and the developer's name in the file name.  For example:

1 - Name contains safeness

Any files that are found can be dragged from the search results window to the Desktop for deletion.

FAF can search areas that Spotlight can't like invisible folders, system folders and packages.

Wow, you're really loaded with apps that are processor intensive. But that aside, Little Snitch, Clam X and SafeNet can conflict with each other, also they are all a constant drain on resources.

Mac needs no additional anti-malware software running. I'd uninstall them. If you want you can turn off CLamX constant scan and just use it as need but I'd dump that too.

Also, the external hard drives may be slowing you down. Disconnect them and after doing all that post another Etrecheck report.

The uninstall instructions for SafeNet are here. Scroll down the page to the end to find them.

https://www.eci.bce.ec/documents/10180/3646060/manualInstalacionOSMacDriverSAC10.pdf/65b45e50-37a0-492f-a8ca-723e6c0a8734

Your EtreCheck report had its formatting scrambled so the report is hard to read, but I also see a few things.

disk2s1 - Macintosh HD

3.12 TB (Shared - 3.01 TB used - 95.47 GB free) APFS

95GB is a fair bit of space but it is only 3 percent of your total storage. Could be slowing things as the computer looks for qualifying drive blocks to write files.

Performance:

System Load: 3.73 (1 min ago) 3.92 (5 min ago) 4.75 (15 min ago) Nominal I/O speed: 15.75 MB/s

File system: 35.47 seconds

Write speed: 48 MB/s

Read speed: 44 MB/s

These read/write speeds are far too low for a 7200rpm SATA 6GBps Fusion drive. We have an entry-level 2011 iMac with a 5400rpm SATA 3GPps hard drive that posts r/w speeds in the low hundreds. Either your hard drive is in jeopardy of failing or all the extra stuff and disk crowding is slowing it. Speeds should be closer to 200mbps.

Some of the PACE software is quite old, and I've heard that it is not very good with newer versions of the macOS. If you really need it, update, If your don't need it or updates are not available, dump it.

If you do another Etrecheck run, try this to preserve the formatting: When you get ready to copy the report, DON'T highlight it. The app takes care of that. Also don't paste it into something else first; paste is directly into an "additional text" box.

I forgot this first time around:

Adware:

Safari Extension: Amazon Shopping Assistant

Reason: Adware name match

Go to Safari menu > Preferences > Extensions and remove it.

Your runtime is unreasonably long and as Allan suggests, it may indicate a failing hard drive.

Also saw in the first report that even with 32B RAM, you were using swap. Now that you restarted it cleared the RAM. Perhaps try restarting more often.

There's no need to defragment a drive at all. Any speed increase you perceived from that is imaginary. Since around 10.2 Jaguar, Mac OS has routinely does that on the fly. Since large files are the ones that get fragmented most they are defragged first.

https://www.macworld.co.uk/how-to/mac/defrag-3600241/

https://www.macbooster.net/how-to/defrag-a-mac-easily

Apple uses the HFS+ (Hierarchical File System), which provides a special function Hot File Adaptive Clustering, or HFC. The main purpose of this component is to automatically prevent fragmentation of disk storage. And it automatically defragments files on its own. 

IMO if you really want to defrag a disk, just copy off the data, wipe it and then copy back.

I really don't know that much about the app, I did a search and it seems to be some sort of VPN. It shows up in a kext file, so you might have a look in /Library/Extensions..