I appreciate the input. Just a little update:
I haven't had a chance to boot a linux live cd (mainly because I don't know much about it) but I have run memtest86 for 4.5 hours with zero errors, ran an extended test with DLGDIAG on the WD drive which passed, and samsung magician is all good.
After observing the behavior more, the freezes increase in frequency and length (still never lasting for more than 5 seconds) the longer the system is on, and more specifically, the longer I work using files on the HDD. Originally I installed all Autodesk products, along with their resources, on the HDD. There's obviously program data/files that get installed to the C drive but for the most part, they're on the E drive. When working on files on the E drive and the freezes are happening, I can open chrome or something that is installed on the C drive, and after a few minutes, the freezes seem to stop until I go back.
Just to test, I uninstalled Revit from the HDD and reinstalled everything to the SSD, including the files I was working on. This seemed to help as the freezes were shorter but they still occurred. There may still be resources the program uses on the HDD as I have several programs and versions (2017,2018,2019,2020) installed and I only migrated one version of Revit to the SSD.
A few things I noticed:
whenever it comes out of the freeze, whatever window I have active, would rapidly flash like it was switching from one window to another (like clicking on and off of a window 10 times in half a second)
It may just be in my head, because now I'm just grabbing at straws, but the read/write noises from the HDD have become louder and more frequent and also occur when idle. I have a "silent" case and I definitely don't remember the drive being this loud. Also, I have no frame of reference, but the drive itself gets pretty hot. But again, when I tested the drive, everything was fine.
One more thing that's always bugged me is the SATA cable going into the HDD has never snapped onto the connector and can easily be pulled out just by jiggling the cable. It's been this way since I built the system but I've tried a few different cables and none of them snap on.
At this point I'm looking at the HDD, the motherboard/SATA controller, or maybe still the CPU, although I'm not as worried about the CPU.
Anyway, I appreciate any help or insight. I realize this issue is near impossible to diagnose from me trying to describe it, and this forum might not even be the right place to look for answers as it might be dealing with specific architectural software installations. But at the very least, I appreciate the space for me to walk around in circles talking to myself, as I really have no damn clue what's going on.
Thanks again.