I've got a bit of a theory here, hear me out and let me know what you think....
The original stereo was earthed through the mounts to the chassis. The new unit, given that it has a separate earth wire, and given that it's an ebay job, would not be expecting to be earthed through the casing/mounts. My theory is that if there is some way that the power supplied to the unit could be earthing through the case/mounts, then that would explain why the stereo and car functioned perfectly when I first connected the earth, but all the faults began after I screwed the unit back into the mounts and out the dash surround back in place.
Plan of attack:
1. Replace blown 140A fuse with stereo completely disconnected. Pray for some function from the bcm.
2. Connect stereo and connect earth to chassis.
3. If the above works, perhaps try some form of insulation between the mounts and the head unit. Ie rubber washers