I wanted to ask you what is your goal with designing your board?
You are designing your own stepper board, which a lot of people do and it is fine with me. However most people do this with the thought that it would be a way to learn about electronics, or they think they will get into the market of selling boards. Some actually think they will save money by building their own. The reality is that the MKS board is very cheap and as such if you are designing a board to sell, your competition is MKS and not me. So people who want to get into this market and sell boards against MKS are in a race to the bottom.
Some think that they will add custom connectors or other hardware that will give them a market advantage. This might be true but to sell a product you have to support it and know how it works. So they are actually again trying to learn.
If you are interested in learning then you are on the right track. Specifically you learn by solving these problems. You learn by testing to see if the motor driver chip is good or not and learning how to do that.
Electrical engineering is not just about math and design, but you need hands on skills. With any discipline that has hands-on skills you need the tools of the trade. Auto mechanics need their tools and electrical engineers need their tools. Scopes, meters, soldering irons, and of course firmware.
It is like being in the construction grading business, you can not grade a road without a bulldozer, and the bulldozer could cost $200k. That is you need the tools of the trade.
These adversities you are having should be embraced and celebrated. For example you have learned that you should never build one unit, or two but the minimum is 3 units because "one is none", two is one. Three gets you two units and maybe some voting. You have also learned if you build 3 boards you need parts for 5-10, that is you will fry parts as you learn. You have learned how to program the bootloader and get the code running. You are doing great, learn how to test the motor, and how to test the motor drivers. Read and understand datasheets. Keep in mind if you are not breaking things you are not learning.
If you have goals beyond learning, let us know so that we can help you there. Again if you want to go into business for yourself and sell boards to a niche market go for it. I initially was upset that MKS did what they did, however I realized that competition is good. Specifically if life had no adversities I would not continue to learn and grow.
So if you want to go into business consider finding the smartest and best competitor you can. For example I will tell you exactly how to compete with me if that is what you want. Actually I guess I did tell you how to compete with me, that is to compete with the smart stepper you need to compete with MKS in a race to the bottom or you learn and innovate new products.