Any version of 3.0 is fine to submit in the 3.0 category, you are all good! Enhanced Edition is the name for the 3.0 Version.

I added patches of the game that I have so that people can use different versions and so that new people can have access to them.

SkinnyJoe64 found that you can not only skip chapter 0 but all chapters in between the last checkpoint. Is this allowed in a run or is there a rule against doing this.

I completely agree with this and I think it would bring new life into the community.