Ok, there is a difference between head height and plumbing length. True head height is actually what the name implies, it's pumping from a body of water at one height to a body of water at a different height. If you had two tanks that were 50ft apart, but were at the same level, then you would technically have zero head height between them, even though you are pumping water 50ft from on to the other. Now, having said that, there is friction, turbulence and obstructions within the systems, and these are resistances to the flow of water. You can't just say that there's 17ft of pipe so there is 17ft of head height. Pipe size, pipe surface smoothness, pressure, etc, also play a part.
It seems that the majority of your plumbing in this setup is 3/4". I doubt that will cause so much of a restriction that it will reduce your flow that much over that distance. Your pump inlet and discharge also sound like they are at the same height, or close, so you have no true head height. This leaves the larger pvc tubes as the last point where such a large restriction can occur. If the type of bio media used is too fine, it will not allow much flow through. Also, if you have sponges and they get clogged up, you will not get as much flow. Lastly, and I suspect this because of how dramatically the flow is reduced compared to where it should be, if you have media in a spot where it can possibly become dislodged and block one of the 3/4" bulkheads, that will obviously reduce the flow a ton.
What media do you have inside the pvc tubes and how are you holding it in place so it cannot block the 3/4" bulkheads you have in place for the water to flow between the tubes?