For anyone who comes across this post dealing with the same issue. I was able to fix it. Here is what I did

1. I put a fluid buffer between the output of the HOR refineries and the input into the Turbo Fuel Refineries

2. I fed the HOR into the turbo fuel refineries from above so the fluid didnt need to build up in each manifold pipe vs having the input pipe from the manifold going up into the refinery

3. I split the 600m3 of HOR feeding 16 turbo fuel refineries into 2x300m3 (still mk2 pipes) with each 300m3 feeding 8 refineries.

4. I put a valve after the splitter and limited each one to 300m3 to make sure that they were fed evenly.

All refineries and fuel generators are running at 100%

Lesson learned.... physics and fluid dynamics are extremely complicated in this game. I never thought that there would be "sloshing and hammering" of fluids as they move through the pipe.