If you're using FSP 3.1.1 and FSO 3.6.10, this is what you should have if you've chosen to install everything:
fsport folder:
FS1OGGcutscenepack.vp, fsport.bmp, fsport3_1_1.vp, fsport-hi_res.vp, fsport-missions.vp, mod.ini, sparky_hi_fs1.vp, stu_fs1.vp, tango_fs1.vp, warble_fs1.vp. There's the readme, but you shouldn't need to worry about that. Also, the settings.ini and data folder are automatically created once the mod is played. Every mod works this way to my knowledge. I also didn't include the new cutscene in the list.
The mediavp folder will have varying contents depending on what type of install you selected.
As an example of proper mod primary and secondary lists, here goes: This is from Silent Threat: Reborn...
[multimod]
primarylist = fsport_mediavps;
secondarylist = fsport,mediavps;
PUNCTUATION IS VERY IMPORTANT! Note that if I want to use the new FSP HTL models I link that folder to the mod in question in the "primarylist." Underscores were highly recommended for mod file names (as per the official FSPort team instructions). Thus, if you have a folder titled "fsport-mediavps," consider renaming it "fsport_mediavps." Naming conventions need to be consistant in both the mod.ini and the actual mod folder. I hope this helped.
-Thaeris