As you know I have the same machine. I have wasted too many hours hammering the gantry back and forth, shimming it, squaring the spindle etc.

When alls said and done you have to realise this is a very entry point hobby machine that we are pushing to its limits cutting aluminium. Being made out of pieces of extruded aluminium bolted together, it moves. It moves with different atmospheric conditions, it moves under load/vibration from cutting aluminium.

In my case my gantry was skewed radially and actually by about 2mm and 1mm respectively IIRC. I've had mine in pieces more times than I care to count trying to make it as good as I can, opening up holes, retapping threads, shimming it. It never stays square for long. In the end I've given up trying to keep everything square as it's a waste of time unless you have an hour to kill every time you set the machine up, and just accept that it is what it is and it makes what it makes.

In your case you can solve the problem of your parts not matching by cutting one side the other way round, then the rhombus will match that of the other half, currently you have them opposing each other. Or you could cut them oversize initially then bolt them together and finish. The ones you've already made could be saved this way.

And in regards to the conversation about controllers, unless OMIO changed controller between my purchase and his it does allow for jogging the spindle anywhere between tool changes, I've never had a problem.