So, I talked to apple support again and did a SMC and PRAM reset. Then I tried the safe mode boot again. It was the safe mode that had the screen flickering. Apps were responding in the exact same way in safe mode as in regular operation. It was the booting from bootable clone where messages turned the screen blank.
I did notice however that really the only thing that is not working is the left click. I can scroll, I can right click, and I can type it seems (I got lucky that I don't need to click to type on textedit; this is what made me realize it is only a left click issue). And right now, it seems to be happening with more apps than less. Chrome, Safari, Office, and Skype are okay still and seem to be functioning okay. I did test an external mouse but it had the same results.
Here is the Etrecheck report, but please not this was after safe boot did not help:
EtreCheck version: 3.0.3 (307)
Report generated 2016-09-12 03:06:02
Download EtreCheck from https://etrecheck.com
Runtime 1:38
Performance: Excellent
Click the [Support] links for help with non-Apple products.
Click the [Details] links for more information about that line.
Problem: Other problem
Description:
Left click not registering on half my apps such as message, App Store, textedit, Evernote, etc.
Hardware Information: ⓘ
MacBook Pro (Retina, 15-inch, Mid 2014)
[Technical Specifications] - [User Guide] - [Warranty & Service]
MacBook Pro - model: MacBookPro11,2
1 2.2 GHz Intel Core i7 CPU: 4-core
16 GB RAM Not upgradeable
BANK 0/DIMM0
8 GB DDR3 1600 MHz ok
BANK 1/DIMM0
8 GB DDR3 1600 MHz ok
Bluetooth: Good - Handoff/Airdrop2 supported
Wireless: en0: 802.11 a/b/g/n/ac
Battery: Health = Normal - Cycle count = 237
Video Information: ⓘ
Intel Iris Pro
Color LCD 2880 x 1800
System Software: ⓘ
OS X El Capitan 10.11.6 (15G31) - Time since boot: less than an hour
Disk Information: ⓘ
APPLE SSD SM0256F disk0 : (251 GB) (Solid State - TRIM: Yes)
EFI (disk0s1) <not mounted> : 210 MB
Recovery HD (disk0s3) <not mounted> [Recovery]: 650 MB
Macintosh HD (disk1) / : 249.82 GB (90.82 GB free)
Core Storage: disk0s2 250.14 GB Online
USB Information: ⓘ
Apple Inc. Apple Internal Keyboard / Trackpad
Apple Inc. BRCM20702 Hub
Apple Inc. Bluetooth USB Host Controller
Logitech USB Receiver
Thunderbolt Information: ⓘ
Apple Inc. thunderbolt_bus
Configuration files: ⓘ
/etc/hosts - Count: 2
Gatekeeper: ⓘ
Mac App Store and identified developers
Kernel Extensions: ⓘ
/Applications/RingCentral Meetings.app
[not loaded] zoom.us.ZoomAudioDevice (1.1 - SDK 10.8 - 2015-12-09) [Support]
/Library/Extensions
[not loaded] xxx.qnation.PeerGuardian (1.1.9 - 2016-09-11) [Support]
/System/Library/Extensions
[not loaded] com.livescribe.kext.LivescribeSmartpen (1.0 - 2016-09-11) [Support]
[not loaded] com.wacom.kext.pentablet (Pen Tablet 5.2.1-3 - 2016-09-11) [Support]
[not loaded] com.wdc.driver.IOFireWireWDHID (1.1.2 - 2016-09-11) [Support]
[not loaded] tl.uds.netusb.controller (1.59 - 2016-09-11) [Support]
Startup Items: ⓘ
HP IO: Path: /Library/StartupItems/HP IO
HP Trap Monitor: Path: /Library/StartupItems/HP Trap Monitor
WDBMService: Path: /Library/StartupItems/WDBMService
Startup items are obsolete in OS X Yosemite
System Launch Agents: ⓘ
[not loaded] 6 Apple tasks
[loaded] 156 Apple tasks
[running] 76 Apple tasks
System Launch Daemons: ⓘ
[not loaded] 46 Apple tasks
[loaded] 159 Apple tasks
[running] 85 Apple tasks
Launch Agents: ⓘ
[running] com.amazon.sendtokindle.launcher.plist (2015-11-13) [Support]
[running] com.canon.MFManager.plist (2012-05-22) [Support]
[loaded] com.citrix.AuthManager_Mac.plist (2013-10-22) [Support]
[running] com.citrix.ReceiverHelper.plist (2013-10-22) [Support]
[running] com.citrix.ServiceRecords.plist (2013-10-22) [Support]
[running] com.huion.HuionTabletConsole.agent.plist (2014-12-25) [Support]
[loaded] com.oracle.java.Java-Updater.plist (2015-01-11) [Support]
[running] com.wacom.pentablet.plist (2009-10-30) [Support]
Launch Daemons: ⓘ
[loaded] com.adobe.fpsaud.plist (2016-04-15) [Support]
[running] com.bombich.ccchelper.plist (2016-03-19) [Support]
[running] com.crashplan.engine.plist (2016-07-13) [Support]
[loaded] com.daisydiskapp.DaisyDiskAdminHelper.plist (2016-03-19) [Support]
[running] com.freemacsoft.appcleanerdaemon.plist (2010-11-06) [Support]
[failed] com.google.keystone.daemon.plist (2010-09-13) [Support]
[running] com.livescribe.PenCommService.plist (2016-04-02) [Support]
[loaded] com.macpaw.CleanMyMac3.Agent.plist (2016-03-20) [Support]
[loaded] com.microsoft.office.licensing.helper.plist (2010-08-25) [Support]
[loaded] com.oracle.java.Helper-Tool.plist (2015-01-11) [Support]
[not loaded] org.eyebeam.SelfControl.plist (2016-04-18) [Support]
[failed] xxx.qnation.PeerGuardian.kextload.plist (2009-03-08) [Support]
User Launch Agents: ⓘ
[loaded] com.adobe.ARM.[...].plist (2012-02-27) [Support]
[loaded] com.citrixonline.GoToMeeting.G2MUpdate.plist (2016-05-12) [Support]
[loaded] com.google.keystone.agent.plist (2016-07-11) [Support]
[failed] com.macpaw.CleanMyMac3.Scheduler.plist (2016-03-20)
User Login Items: ⓘ
Flux Application (/Applications/Flux.app)
TotalSpaces2 Application (/Applications/TotalSpaces2.app)
Flux Application (~/Applications/Flux.app)
iTunesHelper Application (/Applications/iTunes.app/Contents/MacOS/iTunesHelper.app)
Dropbox Application (/Applications/Dropbox.app)
BetterSnapTool Application (/Applications/BetterSnapTool.app)
CCC User Agent Application (/Applications/Carbon Copy Cloner.app/Contents/Library/LoginItems/CCC User Agent.app)
Google Chrome Application Hidden (/Applications/Google Chrome.app)
RescueTime Application Hidden (/Applications/RescueTime.app)
Livescribe AutoLaunch Application (/Applications/Echo Desktop.app/Contents/MacOS/Pen Auto Launcher.app)
Internet Plug-ins: ⓘ
AdobePDFViewerNPAPI: 10.1.8 (2015-01-08) [Support]
Flash Player: 21.0.0.226 - SDK 10.6 (2016-04-21) Outdated! Update
WacomNetscape: 1.1.0-4 (2015-01-08) [Support]
DivX Web Player: 3.2.3.1164 - SDK 10.6 (2014-09-10) [Support]
AdobePDFViewer: 10.1.8 (2015-01-08) [Support]
googletalkbrowserplugin: 1.5.1.10420 (2015-01-08) [Support]
CS ChemDraw Pro: 12.0.2 (2015-01-08) [Support]
iPhotoPhotocast: 7.0 (2015-01-08)
DirectorShockwave: 11.0.3r472 (2015-01-08) [Support]
QuickTime Plugin: 7.7.3 (2016-07-08)
FlashPlayer-10.6: 21.0.0.226 - SDK 10.6 (2016-04-21) [Support]
CitrixICAClientPlugIn: 11.8.2 - SDK 10.7 (2015-01-08) [Support]
CANONiMAGEGATEWAYDL: 3.2.0.1 - SDK 10.6 (2015-01-08) [Support]
Silverlight: 5.1.41212.0 - SDK 10.6 (2016-02-18) [Support]
OVSHelper: 1.1 (2015-01-08) [Support]
npgtpo3dautoplugin: 0.1.43.3 (2015-01-08) [Support]
Default Browser: 601 - SDK 10.11 (2016-07-08)
Flip4Mac WMV Plugin: 2.4.4.2 (2015-01-08) [Support]
SharePointBrowserPlugin: 14.3.9 - SDK 10.6 (2015-01-08) [Support]
WacomSafari: 1.1.0-4 (2015-01-08) [Support]
JavaAppletPlugin: Java 8 Update 73 build 02 (2016-03-13) Check version
OfficeLiveBrowserPlugin: 12.3.5 (2015-01-08) [Support]
User internet Plug-ins: ⓘ
RingCentralMeetings: ZoomBundleVersionNumber - SDK 10.10 (2015-12-09) [Support]
Move_Media_Player: npmnqmp 071503000004 (2009-06-12) [Support]
CitrixOnlineWebDeploymentPlugin: 1.0.105 (2013-04-25) [Support]
WebEx: 1.0 (2008-02-17) [Support]
Safari Extensions: ⓘ
AdBlock - BetaFish, Inc. - https://getadblock.com (2016-06-16)
Adblock Plus - Eyeo GmbH - https://adblockplus.org/ (2016-09-10)
Safari Theme Engine - Brand Thunder - http://brandthunder.com (2015-11-08)
Open in Internet Explorer - Parallels - http://www.parallels.com (2014-01-02)
3rd Party Preference Panes: ⓘ
DivX (2015-01-08) [Support]
Flash Player (2016-04-15) [Support]
Flip4Mac WMV (2015-01-08) [Support]
Java (2016-03-13) [Support]
Time Machine: ⓘ
Skip System Files: NO
Auto backup: NO - Auto backup turned off
Volumes being backed up:
Macintosh HD: Disk size: 249.82 GB Disk used: 159.01 GB
Destinations:
TimeMachine [Local]
Total size: 0 B
Total number of backups: 0
Oldest backup: -
Last backup: -
Size of backup disk: Too small
Backup size 0 B < (Disk used 159.01 GB X 3)
Top Processes by CPU: ⓘ
9% Google Chrome Helper(23)
5% WindowServer
4% kernel_task
2% hidd
2% fontd
Top Processes by Memory: ⓘ
3.26 GB Google Chrome Helper(23)
1.06 GB kernel_task
590 MB mdworker(27)
311 MB mds_stores
229 MB Google Chrome
Virtual Memory Information: ⓘ
7.21 GB Free RAM
8.78 GB Used RAM (3.94 GB Cached)
0 B Swap Used
Diagnostics Information: ⓘ
Sep 12, 2016, 02:54:39 AM Self test - passed
Sep 11, 2016, 10:31:15 PM ~/Library/Logs/DiagnosticReports/Echo Desktop_2016-09-11-223115_[redacted].crash
com.livescribe.LivescribeDesktop - /Applications/Echo Desktop.app/Contents/MacOS/Echo Desktop
Sep 11, 2016, 05:16:33 PM ~/Library/Logs/DiagnosticReports/Finder_2016-09-11-171633_[redacted].crash
com.apple.finder - /System/Library/CoreServices/Finder.app/Contents/MacOS/Finder
Sep 11, 2016, 04:19:31 PM /Library/Logs/DiagnosticReports/Echo Desktop_2016-09-11-161931_[redacted].hang