UPDATE:

So i was able to figure out that I needed a later version of codewalker in order to save the manifest but that seems to not help with the collisions on existing props.
Note I am using an exiting building in the game and existing platforms to create an area for the house but there are no collisions when in game.

So I have two issues currently. One is that when I create my map mod and make sure the flags are correctly corresponding with previous Rockstar models they seem to not work properly in game. Ive used an existing house model but in game I am able to drive through the house, not sure why.
Another issue I am having is when I try to create the _manifest.ymf is will not let me save to at all. So I would have to manually copy it and create a new file and paste it in there. Why is that?