I might not be 100% correct on this, since it has been a while since I did an SH3 mission, but I remember it being the same as in SH4 where the name of the mis file has to match the name of the folder you put it in, otherwise it does not show on the Menu. In other words, you have a mission file you name "SuperMondoCool.mis", which has to be put in a "SuperMondoCool" folder inside of the SingleMissions folder, such that you have "SH3 / Data / SingleMissions / German / SuperMondoCool / SuperMondoCool.mis", or whatever your particular folder structure and language are. Don't forget to fill in the mission parameters... I do not remember how to do the Media.cfg though...