There was in fact a solution to this issue! I asked
@Uwe to reopen the thread to post the final resolution here so anyone who finds this thread in the future can hopefully gain some insight. Sorry for disappearing -- some life issues got in the way and this car sat idle for a while, but it's now a daily driver.
First,
a HUGE thank you to @EuroX and @Dr Sheldon for help troubleshooting! Without you, this likely never would have been resolved and I would have sent the car back under dispute. Instead, the car is running perfectly. Also a huge thanks to the team for providing a tool that can handle everything I've thrown at it related to this Flying Spur.
Solution: The solution to the misfire issue was a
failed #4 fuel injector. The injector may have been mechanically clogged, but the problem was electronic and the injector failed bench testing. This caused the fuel trim issues, as well as the misfire codes.
In retrospect, I believe the reason the misfire codes did not always throw for cylinder #4 is because the misfires are detected by the based on crankshaft acceleration. The deduces which cylinder had a misfire based on the current timing of the engine. As
@EuroX said in
Post #22, the firing order on this W12 is 1 - 12 - 5 - 8 - 3 -10 - 6 - 7 - 2 -
11 - 4 - 9. The misfire codes thrown from cylinders #11 and #9 were likely misfires from cylinder #4, but were sensed as misfires on #11 and #9 because those cylinders fired before/after the real problem. The misfire count for #4 was maxed out, while #11 and #9 were intermittent.
Work done: I replaced all coils and spark plugs (this
YouTube video was hugely helpful). I removed all 12 injectors and took them to an injector cleaning shop for service.
I etched all injectors with their cylinder number to isolate problems. As you can see from the attached images, the injectors were all fine and showed some improvement with cleaning, except for #4 which was dead.
Before / After injector cleaning:

Failed #4 Injector:
I ordered a replacement injector for #4 and put everything back together. It worked perfectly

. No more misfires and fuel trims normalized after driving.
Final Note: In order to get the car to pass emission testing after resetting the engine, all "readiness" checks had to be completed. This involved a long drive cycle (I'll post the link in the manual if I can find it) with lots steps. After that was complete the car passed emissions and there have been no issues with the engine since.
Thanks again to this forum and to the Ross-Tech team for all your amazing help!