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

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Just a quick update, I have confirmed that there is no issue with the frame alignment or ball screw.
I tested the motors when not connected to anything and even on low settings (320,1000,150,0,0)=motor settings.
And they still jam/jar.
so definitely something to do with the electrics/settings.

Good. At least we know that the mechanics are OK. Now change the pulse width to 10. If that doesn't help KEEP it there and change speed to something really low, like 500. If that is still an issue then you probably have a faulty driver card, or a faulty PSU, or both.

I started off with a 3 axis 6560 (blue card). Fixed all the electronic design issues but still managed to fry two before I gave up. In the end I bought a $5 BoB and a handful of DQ542MA drivers and never looked back. My CNC immediately became more quiet, more powerful, faster and with much better acceleration, even though at that time I still had a crappy 24V switched PSU. Changing the driver was the key to success in my case because it solved a lot of issues. That's the route I'd advice you to walk through even if you manage to sort out the current issues. I am still using the same drivers but upgraded the PSU and the CNC in many other ways...