If you've been precise in your statements, your problems started after changing the stock am3+ fan. It seems too uncomfortable to take this as a pure coincidence. I believe that you are missing something. If you are certain that everything is in right order after your final assembly, you should go back exactly after your problem became obvious. Check the motherboards heatsinks! I don't know, maybe some MB heatsink got loose. Just don't loose it and dig deeper. Unless you broke something or something got broke in the mean time, there's should be nothing keeping you from getting the system back to its initial stable state. It's more up to you to figure it out.
I will say this, before I made the initial change the only game that was played on this PC was Minecraft. That game doesn't push the system like a benchmark program or or like the game I used to test, RUST. So I cannot say its a perfect 1 to 1 comparison before and after. I did not test the system with RUST for whatever reason until I changed the first heat sink and fan. So, for all I know it could be possible it was always there and maybe its getting worse. We will see soon enough. Ive picked up another PS, and have an RMA for the current Corsair.