PC is unable to find or locate files which are in the correct location

1. Okay so I've been trying to fix this issue for a LONG time and I've written a lot of posts so to try and give more context on what's happening here's a post I wrote somewhere else explaining the issues I was facing.

"Okay so I'm going to try and keep this as coherent as possible, but basically my computer has been acting incredibly strange. For example I'll launch a program like minecraft through the official minecraft launcher and it won't be able to find my java installation even though I specifically set the directory to the java installation. I tried launching minecraft through a third party launcher and it worked completely fine. Another Issue I get is with league of legends. Every other time I launch it I will have to reinstall it because if will repeatedly crash and the crash logs are empty. If I reinstal it, it'll work fine. Then on steam I get issues with another game where I launch it and I get some error saying "adobe air is not found" and I have to reinstall that game to fix it as well, even though It just breaks and I will have to keep re-installing it. An issue that happens more freqeuntly is not being able to launch any windows service programs without running as admin. (task manager, group policy editor, services, registry editor) I thought this might've been an Issue with my registry so I scanned it with CC Cleaner and another software and repaired all detected errors, but all the issues above still occur. To add more to the insanity I also factory reset the drive where I have windows installed, it TEMPORARILY fixed the problem until 30 minutes after where all the issues listed above started happening again. I can't entirely remember when these things started happening but I think It might've been when I installed malwarebytes and it detected hundreds of false positives for various programs including windows files as well. (anti-cheats for games and other non malicious files) I have no idea what step to take next. I thought about wiping all of my drives but I really really am hoping there is a better solution as my other drive has hundreds of gigabytes of data that I really cant afford to lose right now. Any help is greatly appreciated, thank you."

2. I ended up factory resetting my pc anyways and It's made things much, much worse. Before I would only have to run windows service programs as admin but now it's gotten to the point where If I launch a program that depends on other files. It just wont be able to read that the file is actually there. "Example: ERROR: Could not find Example.exe in C:\Directory\File\Example.exe" And when I'd go to that directory I'd see the Example.exe right in there. This happens with ALMOST every program on my pc. I've factory reset multiple times. Formatted all drives on my pc, booted into safe mode and tried to do an sfc scan but it won't start the necessary service or something like that. Not that it matters though because even before I factory reset the SFC would complete and yield no results.

3. I wonder if this may have made is worse but I changed ownership of my c drive to administrators and am using the default admin account with the same issue.

This is the strangest Issue I've ever encountered.