@SplatHammer I have thoroughly reviewed this thread I don't see how these problems are related to the firmware at all.
Can you please post your config.g and config-override.g file as they exist currently on your duet SD Card?
To be quite frank, your assumption that you have a unique hardware issue related to the design of the board is totally unfounded. Is it possible that your board itself is flawed? Possibly, but even this is rare.
Allow me to offer some further words of advice; if you are using expensive hardware like legitimate hi-win rails, Olson Ruby Nozzles, that sort of thing.... you should develop an appropriate testing procedure in order to minimize damage to that hardware... I would not possibly just 'give it a go' on a design that I am not already vastly familiar with in terms of how it functions with Duet. The Duet Developers and Community are an AMAZING source of assistance, but we all must take ownership to some degree for our own projects.
If you wouldn't mind posting your config.g and config-override.g, which @Danal suggested you do but was seemingly ignored. Please, let us help you by verifying the content of the files.