I am running a mag drive 9.5. It states 950 GPH, I'm assuming that is at 0 head. I have about 5 feet of head on the pump and according to the reef central calculator I should be running about 700 GPH with the head. The scrubber has a 10 inch slot.
Ok, so you are running the scrubber off the overflow, correct?
Here is your error in calculation.
The Danner Mag-drive pumps are rated based on using the correct outlet plumbing. If you read the instructions, you will see that this is 2x the outlet size. In the case of the 9.5, this means you would have to use 1.5" return plumbing to get the rated output per the curve.
If you are using 3/4" return plumbing, which I assume you are because of the corner overflow and loc-line return showing in your last pic, that reduces the actual flow by more than half, due to the physics of flow dynamics. So if you are calculating 700 GPH based on the curve data, I would be willing to bet good money that you are actually at more like 300 GPH if you measured it.
This in and of itself is not likely to be the root cause of the smell. IMO it's a phase. If you could increase the flow, that might help, but it will eventually go away. Part of the reason also is that you have a large screen and little load to "support" it. Once you get past the diatom phase, and you get GHA growing, your screen will not smell while it's running. But that requires that you have enough nutrients to grow all across the large screen.
Did you size your screen according to the tank volume? This is how it appears. Looks like 10 x 10, which is like 8 cube/day on the feeding guideline, but you're probably barely feeding 1 cube/day for now. What I would do is cut a new slot pipe that is 5-6" wide and concentrate all the flow down to that narrower screen, which will increase your per-inch flow rate and give you a more properly sized screen for your tank, which should mean you will grow GHA sooner.