Currently to see what the problem is I need to download your project, create a 3000x3000 transparent image, place it in the project (which may not be in the same position you are using it!), do the export, and compare the the images to your project to see what the actual problem is.
We are happy to help, but there are a lot of things that need our attention. You can make it easier to help you by posting or emailing the first and last image of the animation, as well as screenshots of those exact same poses as they appear in Spine.
Is your 3000x3000 image positioned on integer coordinates? Maybe that helps.
