Use the iso option in tsremuxer, not ts.
You load a playlist, not ssifs manually, into tsmuxer.
Thera are many online guides for tsmuxer. Try the slysoft forum.
If you do look in the ssifs folder, identify the largest file. Its number will be the 3d playlist. So find the playlist with that number and open it in tsnuxer.
Rember, the subtitle issue is not that makemkv loses the depth, its that the player ignores it with mkv. So its easier to make the MVC mkv, and then open that in tsmuxer. That bypasses the whole playlist problem, and creates an iso which will use the depth information inherited from the mkv.