So, just hooked my proper lab scope up and it turns out that the co-relation between the cam and crank sensors shows that the timing (as they report it to the ecm) is 1 tooth out when cold and drifts in to just under 1/2 tooth out when hot. Not enough to trigger a DTC, but clearly enough to effect how it runs.
This despite all the mechanical marks lining up. Apparently this is absolutely typical for a worn lower chain.
Doesn't explain why the engine ran ok in the other car, but have also been told that once the bottom chain wears, it does so extremely quickly.
Hmm, car the engine came from had done 40k miles from new and it had already had the modified top tensioner fitted...