Oh, I didn't realize that the 5V rail was providing 10A. I though you had just stuck a bigger capacitor there in a shotgun attempt to reduce ripple.
With that power level you may have a few other sources radiating noise. It's worth looking at the board and thinking in 3D about the cylindrical antennas (capacitors) and EM projectors (inductors) on the board.
The best way to avoid LC overshoot on the power supply filters is to avoid the L. An inductor kills the transient response and can even destabilize a regulator.
That does seem like the best way
I was trying to avoid the drop of an RC filter, but I guess I can live with losing a volt or two to get rid of these
pesky inductors. I simulated the filter in the schematic above(C is supposed to be 330u), and It goes all the way up to 77V!
I wouldn't be surprised if there are other noise sources. Most of the 5V power is going to charge a phone and to power about 2 meters of LED Strip lighting, which don't seem like they'd produce too much noise. Still, the board layout can use some work in that area.
I guess I'll just put in another 2 stage RC circuit, but to keep the R down I have to have a big cap of ~100uF. I thought that electrolytic caps performed poorly for higher frequencies, is there an alternative type that can handle 36V and performs well across the frequency range. I found some Ceramics, but they're 20 bucks each!