I realize you know that the wiring and routing is contributing to your network reliability problems.
The diagnostic web pages in the PowerFlex 525 might be able to show you if the problems are in the link between the drive and the switch it's attached to (if there are CRC errors or framing errors), and the web pages in the ControlLogix itself will tell you the same for its link to the nearest switch.
But in between those switches.... that's where your network infrastructure is what you need to focus on. Start with a diagram and figuring out which switches can give you diagnostic information.