100% Disk Usage during startup/opening new programs

Hello,
Awhile ago, I was still on Windows 7, and my system began to be incredibly slow, especially during startup. I wasn't sure back then what the problem was, or what I had done to make it so slow. I figured it was linked to BlueStacks, and uninstalling it did help a lot. Startup took about 10 minutes, instead of over 30. However, it was still very slow to open programs, right click, and play games. I thought upgrading to windows 10 might help, but I was unable to because of an error. It only worked after I used CCleaner to fix up the registry. Windows 10 allowed me to see the cause of the sluggish behaviour, as task manager reports 100% disk usage during starup. The problem is, no program in the list actually uses the disk activity, and idles around 0.3MB/sec. It was still always 100%, and only started dropping to normal levels after I messed around with skype (see below for the list of things I tried). Now after startup, if left for a long while, it will eventually finish and drop to idle around 0%. But if I open a program for the first time (ie. WoW, Firefox, Documents, Word etc.) it spikes to 100%. For most programs, it will return to 0%, such as firefox. I am able to browse with no problem, but it will occasionally still spike to 100%, though this seems random. It is most noticable when playing games, such as WoW. If opening for the first time, it spikes to 100%. Some time later it will return to 0%. If I log in, or switch zones when playing, open my bags etc, it again spikes to 100% and makes the game almost unplayable, as it freezes until disk usage returns to 0%. It only behaves this way on lowest settings. If I play on max settings, it almost always stays at 100% (my laptop can easily handle max settings btw). Other games are similar, but the less complex the game is, the less spikes happen. Here is a list of things I have tried to fix the 100% disk usage:
-Turn off tips about windows - no effect
-Turn off BITS - no effect
-Turn of prefetch and superfetch - no effect
-Turned on read/write for skype using the security tab in properties - Disk usage is no longer always 100%, but still spikes as told above.
-Turned off cloud protection and real time protection for windows defender - no effect
-Uninstalled/reinstalled nvidia drivers, and geforce experience - no effect, also worth mentioning that when I restarted after uninstalling, the system took almost an hour to startup, disk usage was again always 100%, and took ages to reinstall the latest drivers. After using CCleaner and getting rid of system files/registry cleanup, the system was as before, 0% disk usage, but 100% spikes.
-Increasing the RAM cache - no effect
-turning off disk fragment scheduling
-Disabling all startup programs - startup takes a lot less time, but disk usage is still 100% during startup
-Disabling all non-microsoft services - no effect
-Check disk using cmd, no errors reported
I installed HD sentinel, and it says disk health is at 98%, with 3 weak sectors, but no action required. Disk temperature is also normal, but if disk usage is 100% for long enough, it begins rising, up to 60+ degrees (C).
Im running out of options, as I've tried nearly everything suggested by google. The only thing that had any significant effect was the read/write enabling for skype, but even that didnt solve the problem entirely. I even tried uninstalling skype, to no avail.
Please help, the new patch for WoW released, and I really want to be able to play normally. Sorry for the lengthy post.

Also, my hard drive is a 1TB HHD hybrid with 16GB SSD.

In case its relevant, I checked the windows event logs, and found 4 errors related to disk.

I also that my net speed drops when disk usage is 100%. So for example, if I refresh a page, the browser waits. The second disk usage is back to 0%, the page refreshes immediately.

Run >> services.msc >> disable windows search and check.
if issue still persists please try a clean BOOT.

I have tried disabling windows search before, had no effect. Here are the results of the chkdsk:

HDSentinel says disk health is at 98% with 4 weak sectors, no action required.
CrystalDiskInfo set health status at caution, current pending sector count 4.

The scan for errors is gonna take a very long time it seems. Its been going for about 2h with only 2 rows complete. Seems like it needs over a day straight to finish. Will post back the results here if it ever finishes, along with everything else. The scan speed fluctuates between 50MB/s then steadily drops, and disk activity is 100% the entire time, explains the slow progress.