I don't have time to actually quote you now, so I make it a little more point by point. I have to go to sleep now.

Either way, what you should do is make a copy of the maps and system trees, call them like mapsold and systemold, then edit the ini files meaning Unreal.ini or you can make a custom ini but you'd have to specify that with -ini, let's just make it simpler for you then.

Just in the new directory change Unreal.ini paths in the Core.System section into SystemOld and MapsOld instead of plain System and Maps.

Then in systemold and mapsold you just extract those archives that were there like maps and system and let it overwrite the files it has conflict with.

Well, that's basically it. It's so simple and yet most mods or tcs out there for unreal etc don't even do this.

And now for the other questions.

Yes I provided all the original new archives plus the old leak plus fixes/tests made by me, all in sepearate archives of course.

The chronology goes like:
zipped 224 compatible files - plain 224 jazz 3d - 400 calypso - the known leak

So the known leak is the latest there was. And there isn't that much difference indeed between 400 calypso plain and the leak...

As for you wondering, I can assure you that there is little to no chance of anything more turning up from the same source(s), but of course I haven't spoken to most people who worked on Jazz 3d even, so who knows.

If you find some, try to reach out and ask.