Update, I used smart UV unwrap after I combined all objects and it has corrected the orientation. But I would still like to know if there is another way to do this because I have used smart UV in the past and its hit and miss. So I was wanting to know if there was a way to pack it with all the uvs I have already unwrapped while keeping that same orientation.
This is my color ID map, everything is still split into pieces all over, id prefer if they were all next to eachother. This is another problem I am having. Is there a way to get them all lined up without manually doing it?
*Edit is there also a way to combine all objects without combing all the modifiers*