Installed a set of mods but all of them state the Manifest file is missing.

i had the same problem, check your mods folder, if the folder names of the mods have numbers at the end it means the directories containing the mods are too deep.

here's what i did, i made a folder on my desktop named misc, then i moved all of the folders out of the COI mods folder into this misc folder.

if you notice, each of these folders has a version number, the actual mod folder is inside these folders
for example

see how that folder doesn't have the version number? that's the folder you want to drag into the COI mods folder, not the one with the version number.

then restart your game and try to add the mods again, i hope this helps