Off the top of my head (bit fuzziheaded)
Uninstall game, use your way to check for game remnants and remove
Install game/patch to 1.2
I reboot after each (no idea if really needed, doubt it lol)
Install the generic patcher and sort to my liking/needs
Create a folder in sh5 directory called MODS (not with jsgme) sometimes do this before installing the g/patcher
Start vanilla career, do tutorial, get to kiel, listen/wait/then exit from bunker and game
Install mods/Install Options File Viewer, set to wants/needs
Check any menu/cfg's i might have to alter that require a career start
Load game, load bunker save
Start baltic operations knowing pain is coming my way lol
added a link .......
http://www.subsim.com/radioroom/showthread.php?t=180044 may help, dunno if the videos are helpful i haven't tried them