Hi @Anonymous, thanks for your post!
A quick caveat: We cannot help with engineering design and I do not want you to make design decisions based on conversations with our support team. That being said, I will attempt to help you understand how the model is working as you have currently configured it.
I took a look at your model; thanks for providing it! To answer your questions:
1. MH-3 is flooding and Link-04 is surcharging. This makes sense as you have set the outfall fixed elevation so high. You've modeled a backwater situation where water is flowing back up the system to elevation 69' and mixing with the water coming from the basin which peaks around 20 min as you said. You can see this by looking at the time series plot of Link-04; the negative flow shows the water flowing upstream. If this submerged tailwater condition reflects reality, then so be it. If not, then change the outfall boundary condition.
2. The flowrate is decreasing because the flow rushing downstream from the basin encounters the backwater from the outfall tailwater.
As a general modeling note, I would change the outfall boundary condition unless that reflects existing conditions. To model existing flow coming into MH-3, the ideal way would be to create an existing model with basins, structures, pipes, etc and connect those to MH-3. If this is not feasible, you could also add a user-defined external inflow to MH-3. You could add a constant flow or add a time-series to reflect the existing time series flowing through MH-3 if you have data for that.
All the best,
Winston