1. The logs are present, but the part where the system databases are upgraded is missing from the logs for the instance that failed.

2. Correct. It shows that it is upgraded to SP4 on every node when you fail it over to any node in the cluster, but none of the system database upgrades happened.

The binaries are all patched and match, but I know the patch wasn't 100% successful since the system database updates were missed. I am just taking a chance that with me updating the system databases manually and that the binaries were patched, that we won't run into any issues, but there is no guarantee that other things weren't missed.