You have changed the breakout board - but I am sorry to say that (from thepicture you supplied) you got the cheaper non-isolated version. This is fine, if you have a good knowledge of electrics.
The isolated version of the card splits the card in two electrically, and provides two seperate power inputs - one which you can power from your computer, and one which you can power from your driver board supply.
The board you have bought does not do that. I must urge you again to provide a seperate supply for your breakout board. Not one derived from your driver cards, or one derived from the computer. It can be a plug in telephone charger (if it is the right voltage) or a games console power unit etc - BUT at least it will be electrically isolated.
You are still going for the big bang - good luck
My approach, if I was a little unsure what I was doing, would be to do each part seperately, and certainly connect each axis seperately. I did that when I was starting, and ran everything on my workbench, before trying to assemble a full box of electrics. I have only just now finished my electrics box, because I think of something else to add, and I have been messing around with computers and electronics and electrics for nearly 50 years.
You picture looks very good - but without a wiring diagram of where you have put all the wires, and where the power comes from, I cannot give any opinion.