Where is the fountain of knowledge for learning about CNC setups / understanding them

[m_c]

Going by the picture, K1 and K2 set the microsteps.
K3 and K4 set standby current.
And the SW set motor current.

If the new computer has made no difference, then that should rule that out.

You've got nothing to lose by trying with the motors disconnected from the machine.
What's making me think it's not mechanical, is the seemingly random position the thud occurs, and that it affects more than one axis. If it was something like a bit swarf in a ballnut, I'd expect it to stall completely until the direction is reversed. I'd also expect to be able to feel something moving it by hand. You could perhaps try running the screws with a cordless drill and see if you can feel anything, as something like swarf may only show itself at speed.

However, to me it sounds more like a glitch in the electronics side. My next step would be to try a different power supply, or hook up an oscilloscope to see what was going on.

To answer your previous post, don't get an all in one system. Get a separate BOB, and if funds are really tight, get some of the basic TB6560 stepper drives. They're far from high performance, but they'll match what you've got, and individual drives can be swapped later if needed.