why are you moving the log files for the system databases, except perhaps for TempDB there is nothing to be gained by doing that, and a lot of potential heartache to be had.

Replication does not care where the log files are and you will have to quiesce the app to move the files anyway so I don't see any issues there, though I admit to not having done it.

you don't state how you are moving the log files but I strongly recommend using alter database..modify file along with offlining the database whilst you move the file, so there is no need to restart sql server to achieve that.

back the databases up first.