LoTV should have all the stuff HoTS, and WoL have and more, just with slightly different balancing. So you should only need to add LoTV, and the campaign data if you want that. See picture for the dependencies I would go with.
For the upgrades:
- Presentation wise: I would probably follow other campaign that have map loaders. Often map makers will make one file that is purely for loading up missions. They'll create little scenes in these maps that represent what the mission will be about. The camera looks at these scenes when clicking a button. Then when hitting load or play, it'll jump to the new map file. You could make little scenes and UI for your upgrade menus.
- Behind the scenes: You'll want to look into using "Bank" files. Go here: https://sc2mapster.gamepedia.com/Tutorials and do a search for Banks. Not much has changed, so even old tutorials are fine. Banks are just text files that get saved to the players computer and can include things like integers, booleans, and some other variables. So when a player is interacting with your upgrade UI, you can create a bank file. Your maps can then read that bank to see what upgrades they chose, you then activate them in your map.