Permission error replica set
Usually the cause for this is that you are restart the mongod process as the root user (using sudo, or perhaps invoking directly as root) or some other user besides the appropriate MongoDB user (in your case mongod).  That is then screwing up the permissions in your data folder and giving you the error you are seeing.

If you examine how you are starting/stopping the process and correct it to only start with the correct user (or use the service commands instead) then this problem should stop happening.