Safari was extremely slow to open after I ran this program, will note. Normally Safari opens with no other problems, so I thought I should mention that...
Also, I read the information you linked, but I don't have any extensions, and a lot of the other stuff checked out.
EtreCheck version: 3.4.4 (448)
Report generated 2017-09-02 14:57:27
Download EtreCheck from https://etrecheck.com
Runtime: 3:48
Performance: Good
Click the [Lookup] links for more information from Apple Support Communities.
Click the [Details] links for more information about that line.
Problem: Other problem
Hardware Information: ⓘ
Mac mini (Late 2014)
[Technical Specifications] - [User Guide] - [Warranty & Service]
Mac mini - model: Macmini7,1
1 1.4 GHz Intel Core i5 (i5-4260U) CPU: 2-core
4 GB RAM Not upgradeable
BANK 0/DIMM0
2 GB DDR3 1600 MHz ok
BANK 1/DIMM0
2 GB DDR3 1600 MHz ok
Handoff/Airdrop2: supported
Wireless: en1: 802.11 a/b/g/n/ac
Video Information: ⓘ
Intel HD Graphics 5000 - VRAM: 1536 MB
NXM76LCD 1280 x 1024 @ 60 Hz
Disk Information: ⓘ
APPLE HDD HTS545050A7E362 disk0: (500.11 GB) (Rotational)
[Show SMART report]
(disk0s1) <not mounted> [EFI]: 210 MB
(disk0s2) <not mounted> [CoreStorage Container]: 499.25 GB
(disk0s3) <not mounted> [Recovery]: 650 MB
USB Information: ⓘ
USB30Bus 1 TB
TOSHIBA External USB 3.0 1 TB
Mitsumi Electric Hub in Apple Extended USB Keyboard
Microsoft Microsoft® Comfort Mouse 4500
Mitsumi Electric Apple Extended USB Keyboard
Apple, Inc. IR Receiver
Apple Inc. BRCM20702 Hub
Apple Inc. Bluetooth USB Host Controller
Thunderbolt Information: ⓘ
Apple Inc. thunderbolt_bus
Virtual disks: ⓘ
Macintosh HD (disk1 - Journaled HFS+) / [Startup]: 498.89 GB (420.48 GB free)
Physical disk: disk0s2 499.25 GB Online
EXTERNAL HARD DRIVE (disk2s1 - Journaled HFS+) /Volumes/EXTERNAL HARD DRIVE : 1.00 TB (858.78 GB free)
Physical disk: External USB 3.0 1.00 TB (858.78 GB free)
System Software: ⓘ
OS X El Capitan 10.11.6 (15G1611) - Time since boot: about 16 hours
Gatekeeper: ⓘ
Mac App Store and identified developers
Startup Items: ⓘ
TuxeraNTFSUnmountHelper: Path: /Library/StartupItems/TuxeraNTFSUnmountHelper
Startup items no longer function in OS X Yosemite or later
System Launch Agents: ⓘ
[not loaded] 7 Apple tasks
[loaded] 153 Apple tasks
[running] 78 Apple tasks
System Launch Daemons: ⓘ
[not loaded] 46 Apple tasks
[loaded] 152 Apple tasks
[running] 92 Apple tasks
Launch Agents: ⓘ
[loaded] com.google.keystone.agent.plist (Google, Inc. - installed 2017-07-10) [Lookup]
Launch Daemons: ⓘ
[running] com.adobe.agsservice.plist (Adobe Systems, Inc. - installed 2017-05-29) [Lookup]
[loaded] com.adobe.fpsaud.plist (? 2afb3af7 85012398 - installed 2017-07-24) [Lookup]
[loaded] com.google.keystone.daemon.plist (Google, Inc. - installed 2017-07-26) [Lookup]
[loaded] com.macpaw.CleanMyMac3.Agent.plist (MacPaw Inc. - installed 2016-07-19) [Lookup]
User Launch Agents: ⓘ
[loaded] com.macpaw.CleanMyMac3.Scheduler.plist (MacPaw Inc. - installed 2017-07-28) [Lookup]
User Login Items: ⓘ
Flux Application
(/Applications/Flux.app)
iTunesHelper Application (Apple, Inc. - installed 2017-07-22)
(/Applications/iTunes.app/Contents/MacOS/iTunesHelper.app)
CleanMyMac 3 Menu Application (MacPaw Inc. - installed 2017-01-04)
(/Applications/CleanMyMac 3.app/Contents/MacOS/CleanMyMac 3 Menu.app)
Internet Plug-ins: ⓘ
FlashPlayer-10.6: 26.0.0.151 (installed 2017-09-01) [Lookup]
QuickTime Plugin: 7.7.3 (installed 2017-09-01)
Flash Player: 26.0.0.151 (installed 2017-09-01) [Lookup]
Default Browser: 601 (installed 2017-08-29)
o1dbrowserplugin: 5.41.3.0 (installed 2016-07-13) [Lookup]
googletalkbrowserplugin: 5.41.3.0 (installed 2015-12-11) [Lookup]
Silverlight: 5.1.40728.0 (installed 2015-09-26) [Lookup]
User internet Plug-ins: ⓘ
CitrixOnlineWebDeploymentPlugin: 1.0.105 (installed 2013-04-25) [Lookup]
3rd Party Preference Panes: ⓘ
Flash Player (installed 2017-07-24) [Lookup]
Tuxera NTFS (installed 2015-06-18) [Lookup]
Time Machine: ⓘ
Skip System Files: NO
Mobile backups: OFF
Auto backup: YES
Volumes being backed up:
Macintosh HD: Disk size: 498.89 GB Disk used: 78.41 GB
Destinations:
EXTERNAL HARD DRIVE [Local]
Total size: 1.00 TB
Total number of backups: 65
Oldest backup: 6/18/15, 9:15 PM
Last backup: 9/2/17, 2:51 PM
Size of backup disk: Adequate
Backup size 1.00 TB > (Disk used 78.41 GB X 3)
Top Processes by CPU: ⓘ
23% update_dyld_shared_cache
5% kernel_task
3% WindowServer
0% mdworker
0% fontd
Top Processes by Memory: ⓘ
985 MB update_dyld_shared_cache
441 MB kernel_task
111 MB softwareupdated
61 MB WindowServer
60 MB system_installd
Top Processes by Energy Use: ⓘ
54.22 update_dyld_shared_cache
3.64 WindowServer
0.42 softwareupdated
0.40 mdworker
Virtual Memory Information: ⓘ
2.41 GB Available RAM
1.02 GB Free RAM
1.59 GB Used RAM
1.39 GB Cached files
149 MB Swap Used
Software installs: ⓘ
Adobe Flash Player: (installed 2017-08-09)
Adobe Flash Player: (installed 2017-08-29)
Adobe Flash Player: (installed 2017-09-01)
Install information may not be complete.