mac pro 4.1 early 2009 el capitan vs high sierra OS performance

The runtime for your report is 5 minutes 18 seconds. That number is WAY too large. Your Mac is too slow.

My Mac Pro 2.93 with four cores at 2.93 and a rotating magnetic drive (way slower than your SSD drive) completes the Etrecheck 5.2 report in 2 minutes 43 seconds.

Major Issues:

Anything that appears on this list needs immediate attention.

Unsigned files - There are unsigned software files installed that could be adware and should be reviewed.

one in particular is flagged as "possible adware" and may not be what it purports to be. It should be deleted, as it is not needed anyway.

Heavy CPU usage - Some processes are using an unusually high amount of CPU.

The amount of CPU being used by Final Cut, the Apple encoder, and the Apple decoder is very large. If you are actively processing video, that may be OK. If not, something is terribly wrong.

Minor Issues:

These issues do not need immediate attention but they may indicate future problems or opportunities for improvement

.

Heavy RAM usage - This machine is using a large amount of RAM.

Clean up - There are orphan files that could be removed.

System modifications - There are a large number of system modifications running in the background.

The number of User login items is enormous, and ALL should be removed.

That version 3 of Etrecheck in an antique. The current version 5 is much better.

NVIDIA GeForce GTX 980 - VRAM: 4096 MB

Nice graphics card. But not approved for use in Mojave:

Install macOS 10.14 Mojave on Mac Pro (Mid 2010) and Mac Pro (Mid 2012) - Apple Support

TOSHIBA-TR150 disk1 : (480,1 GB) (Solid State - TRIM: No)

Nice SSD drive. But you need to turn on TRIM, then run it once in Safe Mode to clean out the deleted data.

Sudo trimforce enable

https://www.lifewire.com/enable-trim-for-ssd-in-os-x-yosemite-2260789

Unknown Files: 􊋏

/Library/LaunchAgents/com.Gjaqbmwt.plist

/Library/LaunchAgents/com.almoner.plist

/Library/LaunchAgents/com.tonetically.js.plist

/Library/tonetically.js/tonetically.js.app/Contents/MacOS/tonetically.js

/Library/LaunchDaemons/com.ScCnuPsU.plist

/Library/LaunchDaemons/com.adobe.acc.installer.plist

/Library/PrivilegedHelperTools/com.adobe.acc.installer

/Library/LaunchDaemons/com.apple.riarat.plist

/Library/riarat

/Library/LaunchDaemons/com.hcdrkswmlbzm.plist

/Library/LaunchDaemons/com.nvidia.cudad.plist

/Library/Frameworks/CUDA.framework/Versions/A/Resources/cudad

~/Library/LaunchAgents/com.lactim.plist

/var/root/Library/lactim/lactim

~/Library/LaunchAgents/com.mortmain.plist

/Library/mortmain/mortmain

10 unknown files found. [Check files]

The newer version know what those files are. Some look like adware amor worse to me, but Etrecheck 5 has better advice.

Kernel Extensions: 􊋏

/Library/Extensions

[not loaded] com.FTDI.driver.D2XXHelper (1.0 - SDK 10.11 - 2017-12-15) [Support]

[not loaded] com.sony.filesystems.pdudf (5.07.0d019 - SDK 10.6 - 2017-12-15) [Support]

[not loaded] com.sony.filesystems.pdudfr (5.07.0d019 - SDK 10.6 - 2017-12-15) [Support]

[loaded] com.sony.scsi.PDW-U1 (5.07.0d019 - SDK 10.6 - 2017-12-15) [Support]

/System/Library/Extensions

[...]

[not loaded] com.sony.filesystem.prodisc_fs (2.3.2d12 - SDK 10.0 - 2017-12-15) [Support]

[not loaded] com.sony.protocol.prodisc (2.3.2d12 - SDK 10.0 - 2017-12-15) [Support]

[not loaded] com.wacom.kext.wacomtablet (Wacom Tablet 6.3.15-3 - SDK 10.11 - 2017-12-15)

I don't see the Hardware these extensions support.

There are more individual items junk installed that are not appropriate, but are not necessarily evil. "Junk" in this context means things that may be perfectly good, bi=ut you don't happen to need right now, like things stored in the attic.

You would be better off doing a clean install after erasing the drive. You will need the the cuda extensions to get a accelerated picture on the display.

This is what Apple says the previous owner SHOULD have done for you:

What to do before you sell, give away, or trade in your Mac - Apple Support

.