Well, excellent thread, so thank you for taking time to share your experiences. I am afraid that I might be in a similar situation.
I have been doing “projects” on 2009 4.8 X5 for the last couple of weeks (stem valve seals, coolant pipe, cleaned injectors, oil thermostat gasket, obviously all new seals:valve covers, timing chain covers, spark plugs, etc.). Assembled everything yesterday, but got misfires

- uneven idling and impaired acceleration. I wiggled the coils, but no change was observed. My plan is to connect to ISTA to see specific codes and what cylinders misfire and then try to swap spark plugs, coils, and listen to injector “clicking” for a troubled cylinder (s). If unsuccessful, I might need to do the compression cylinder test like you had done and then probably take the valve cover off and inspect the keepers and stem stem valve assembly.
So, in your case, on cylinder 1, the incorrectly installed keepers were not visible and were under the retention plate? Was this valve moving differently compared to others when rotating the engine? What else to look for in stem valve assembly? I assume I would need to take all spark plugs out to prevent hydro locking the engine when rotating - is that true? Had seen it in some stem valve seals video...would rather skip if that is unnecessary.
Also, if you could share some details for cylinder compression test it would awesome since I have never done one myself. What equipment to buy? Thanks in advance!