So Ive searched the forums about this and it seems that the majority of people who have posted about this are only building skirmish maps. And thus far I have only been able to glean bits and pieces of information but nothing really substantial that helps at all.
If this isnt too big an issue: How would one make the AI build and function normally (or rebuild existing...), as it would in a skirmish map, on a mission map?

Use the build menu
The reason people aren't asking about this is because it's pretty simple and common sense.

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On the topic of Build List, when you double click a structure in the list, what specifically does the