So after hours of banging my head and wondering what i was doing wrong... I finally have the xyz motion working as expected. Allow me to share a few things I learnt on the way.
1) Use a known good to begin with Dan's frankencube marlin install for example
2) If things still go wrong odds are something is
**** up
- I over tightened one of the limit switches so it never registered as having reached it limits.
3) Thermal paste is conductive
I hope someone gets a chuckle at the torture i went through today.