Pretty sad to hear this is still going on Martin.
Never mind the insane registration and insurance charges where you are. We are relatively lucky here, with my Ducati's registration (and compulsory third party personal insurance) totalling $478. The 750 Cagiva's now $357, but I am now in a 'rural location' about 60 miles out of Adelaide. But yes - like the Californians we get to ride year-round.
Back to your valve timing - clearly the timing needs to be checked, with regard to key locations, from top to bottom.
Please get your work checked by someone who really knows, with the actual cams and rockers exposed, before running it again. The timing marks on the camshafts change between models, so this is not a 'one size fits all' knowledge.
An actual visual check of cam positions (at both TDCs, on both cylinders) is vital with the changes in camshafts over the models. You are certain that all four cams are original, and from the correct model? A for aspirazione on the intake and S for scarico on the exhausts. (And of course the inlet/exhaust cam position is reversed on one head against the other).
Do a check using the actual TDC - checked via the plughole - rather than relying on any marks.
But, as you said, if only one cylinder is out of time (and you are certain of this) it has to be from the paired pulleys on the right-hand end of the crossover shaft, or above.
I have seen an Ergal pulley that damaged its keyway when it wasn't tight enough, but it never actually lost its timing - just developed play back and forth. But a close scrutiny of these keys and keyways probably a good starting point.
I prefer to refer to the 'half-time shaft' as a crossover shaft on these engines rather than a layshaft, as a layshaft tends to refer to the shaft in a gearbox which has neither the input (primary drive/clutch) nor output (final drive sprocket) mounted on it, like that in the old bevel engines.
Not trying to be pedantic here as much as be clear on what we're actually referring to.
All the best with it Martin. Pretty ordinary that the business who helped you with it can't simply fix the problem they didn't fix as a matter of responsibility, rather than trying to turn it into another money-making opportunity!
I would have expected your consumer protections to offer some support with this (and your previous situations) but of course I'm in a different country, and have rarely had to get a shop to do any work for me.
You may think "well bully for you!" but in reality this lifetime of working on motorcycles has not made me wealthy - only knowledgeable and with dirty fingernails...
And with a lifetime of reliable Ducatis! Sorry I can't offer any more help from this distance. Surely you are close to sorting this..?