Uh sorry guys, there was a misunderstanding.
The maximum number of buildings is 64 * 9 = 576 (9 buildings for each of 64 complexes)
I said about 400 because I estimate there'll be a loss of about a third of the building slots because we can't use each complex to its full complexity (if you excuse the pun), and some building complexes probably will have only 5 buildings in them.
You can't link upgrades to different building trees because every upgrade has to be listed in the level line after the building you are doing the upgrade for.
That means:

levels building_1 building_2

Another complex:
levels building_3

building_1 can have building_2 as an upgrade but building_2 can't have building_1 as an upgrade.
Both can't have building_3 as an upgrade and vice-versa.