So I have solved almost all cooling problems with this computer by basically gutting it and putting in all new hardware; liquid cooling(which it said on the box it was supposed to have but came with a fan), hard drives, power supply and GPU. But I haven't changed the front fan.
I got a MSI Gaming GeForce RTX 2080 Aero for the new GPU after trying out many cards and combinations of linked cards that just wouldn't fit in this tight rig. Once I was able to get this one in, it was tight and it gets hot but I was happy. I never tested with the old gpu either if the fan actually did anything but I noticed the other day when trying to reduce the jet engine noise coming from the front fan when gaming that the front fan had no change on the gpu temp, from 0%-100%.
During tests when I was overclocking with high in game settings the GPU was at 88c turning the front fan off changed nothing and turning it to 100% also nothing, steady 88c.
Reducing graphics settings but staying overclocked GPU is at 81c and again front fan 0% or 100% makes no difference.
Turning off overclocking and using high graphics settings GPU is steady at around 75c and front fan does nothing 0%-100%.
Idling while typing this post the GPU runs at 54c turning the fan on or off again makes no change.
All side panels are closed and locked and back plates are in. My power supply uses some pretty hefty cables that could definitely be blocking airflow, that is the only thing I could think of that would cause this. But they are not between the GPU and the front fan. And shouldn't cause the fan to have no effect.