I have removed the cooler, cleaned the dust out, wiped the old paste off the GPU, put fresh thermal paste (artic silver) on the GPU and put the cooler back on. I have also notice the HDD IDE cable was blocking the cool air from getting to the GPU cooler. I have also cleared away the dust from the CPU, PSU, HDD, AGP slot, motherboard. I tried to round the floppy cable for better air flow. Lastly I removed the one back plate so the GPU cooler can blow the hot air out of the back of the case.
Running the system idle and GPU-Z reports PCB is 42C and GPU is 45.6C.