First of all I would like to thank SpaceInvaderOne for his excellent videos!!!
As far as the wrong time zone, mwells suggestion works but it is not persistent across reboots of the container.
I have added the following path to the container. This seems to have fixed the problem with time.
Also regarding the config file being erased across reboots I have placed the conf.json file with my changes inside the appdata/shinobi_pro folder.
Thank you!