As I’m looking at this in my minds eye, that missing spacer would bow in the left hand plate. That bow is then effectively acting as a spring, that could it be trying to pull the cradle over one way or another depending on what it’s levering against?
I would also ask, is it correct to assume that only the left hand plate got bowed? Could the RH plate also get pulled in and distorted, further complicating things?
When you replace that missing spacer, unless you have identified and straightened ALL distortion PERFECTLY, then the issue of the distortion pulling things over probably remains, in fact would likely be made worse by the addition of the spacer if some distortion remains.
So, in summary, I would personally be thinking that the missing spacer - distorted cradle - high vibration topics are all linked.
I know Commandos are rather crude by modern standards, but to function as intended, that whole engine / cradle / ISOs / frame relationship needs pretty good alignment IMHO.