Hi Trevor,
I think the misalignment must be due to the pivot bearing/clutch arm combination. The bell housing and engine back-plate are the same ones I used with my previous Magnette engine and clutch. The only problem I had then was a slight tendency to clutch slip on first engagement.
When I fitted the 1800 engine I decided to change to the MGB diaphragm spring clutch and Peter Gamble supplied a new pivot bearing and an MGB clutch arm to suit. It was only after that the problems started. You may remember I found that the slave cylinder push rod was not acting perpendicular to the clutch arm and I had to add a 5mm spacer under the slave cylinder to correct this. There also appeared to be too much throw on the clutch arm so I fitted a stop under the pedal to limit this.
I did discuss these issues with Peter but he said he had not heard of them before.
The inspection camera pictures are not really good enough to properly understand what is going on. The field of view is too narrow and manoeuvring the camera too hit and miss. It does seem clear however that the carbon thrust approaches the pressure plate at an angle and hits it first at the bottom, not realigning itself properly when it does so until considerable force is applied.
I cannot really visualise what could be causing this, so I am afraid the only way to resolve it will be to have the engine out again!
Andy