Ported the mods to 2.0 on my system, and can play it fine in SP.
Tried uploading them to my usual factorio server, and they fail to initiate/load. All other mods load fine, just the updated ones do not.

According to the servers output , the "info.JSON" file cannot be found, for any of the mods ported with this tool.
But the files exist, the mods work fine in singleplayer , and from a quick comparison, the info.JSON files follow the same/correct format , as other mods (which the server does load)

My first thought is that your server setup is trying to update the mods from the Portal, and because they don't exist, it's failing.

Without extra information, this sounds like a user-specific issue.

It's a Factorio instance running on an AMP Instance on a rented machine.
From what I can tell, and past experience, the server has never tried to automatically update or even verify any mods we ran on it.

"Error ModManager.cpp:1140: Mod package read error. File mods/IndustrialRevolution3_4.0.0.zip/info.json not found" is the full error message, with one of them for each of the ported IR3 mods.

I would take that error message at face value, and assume that the info.json is either missing or corrupted, and that the mod files on the server and the client are not the same.

Do you get different results if you deploy the mods extracted as directories, rather than being in ZIP format?

I checked, and double checked.. the files are identical (I uploaded them from my client afterall..).

I believe I have fixed it though. I unzipped each of the mods, and copied the info.JSON up one directory , so it is now in the "opening folder" of each zip.
Server loads them just fine now. No clue why, none of the other mods have said file in that location.. but it works \o/
Now all I am faced with is "Error Util.cpp:81: Error in assignID: fluid with name 'concrete-fluid' does not exist." , but I doubt that is relevant for here.

While I got your attention, I wanna say thanks for making this publicly available tool for everyone to use. IR3 is by far my favourite overhaul, and I have dearly missed it since 2.0 released! Thank you!!