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

[m_c]

Something about the ballscrew/bearings does sound a bit dry, but nothing I'd worry too much about. They don't actually need that much grease, as too much grease can be as bad as too little grease.


Did the parallel port (latency?) test pass OK?
Those clunks could be cause by a glitch in the pulse stream, which is often something causing an interrupt on the computer. I'm going to assume you've done the basics, like ensure all non-essential software has been removed/disabled (that includes any anti-virus).
I'd re-run the parallel port test, and see what results you get. Some hardware configurations are just not suited to running the parallel port for motion control.