I've shared in your pain, I have a rig that should be able to blast through this game no problem. Long loading times and NPCs failing to load for quite a bit after I've arrived at their locations were the beginning of a problem that was caused by a failing HD. I'm not sure about CPU throttling, I never really looked in that direction.

However in most cases of players reporting long load screens on a machine that should perform well in the game... the answer typically always fell in the HDD department. Weather it be age, failure, defrag or low IOPS.

Maybe share all of your hardware with the community and they could help you find a more direct lead to your issue.

In my case the game performs just fine once it does load, but loading is horrid. I'm not sure we suffer from the same issues, but maybe it's something you can look into.