I'm actually ABLE to repair the drive but the repair fails and basically says to backup whatever I can and get a new drive...
I had the same issue last year, also random beach balls started getting more frequent. Can you access the Console Log? Are there are any errors around disk i/o? I had a few errors like these. What is the SMART status of your hard disk? (I had used the smart-utility to check this).
I ended up re-installing everything, but the issues came back. I run some disk diagnostics tools, which marked a few blocks as bad, but every time I was running these tools, they kept marking more and more bad blocks. The SMART status was also failing.
In my case, it was a clear and simple failure of the hard disk. I asked

how much it would cost to get it replaced, they quoted me a stupid price, then I went out and ordered a Seagate 750 hybrid, for much less money, put it in, installed OS, happy days...
I hope it's just the software, but it does not seem so... If the reinstall fixes your problems, then fine, but if they keep coming back, this is almost sure HD failure, it happens...
😱