I want to make it so that when a player builds an Academy, the academy is removed and switched to a Computer's Bunker (P7) with 2 marines taht will be loaded onto the bunker..

Then, I want the bunker to turn into the state where when you click it, it says it's "Disabled" like a protoss building w/o pylon, and is cloaked, and still be able to attack.

In my triggers, i used "Disable bunker" and then "Enable bunker" .. so Disable+Enable .... It works for some bunkers, and some of the bunkers are just Disabled, where they don't have the "Disabled" phrase, and don't make that cool turning-a-building-off sound when you click on it, and is cloaked differently (Only seeable if you control the bunker, but can't see the bunker if it's owned by the computer even if the shared vis is on)

Just load them in and use disable doodad state once. I think that's what you mean.

yes...
Complete Trigger:

Player: X
Condition: PLAYER commands at least 1 Academy (or bring to "battleffield")
Action: Preverse Trigger
Action: Move Location Y on Academy owned by PLAYER
Action: Remove Academy owned by PLAYER at Y
Action: Create 1 Bunker for PLAYER at Y
Action: Create 2 Marines for PLAYER at Y
Action: Run AI-Ascript: enter closest Bunker at Y
Action: wait 50 MS
Action: Dsiable all Bunkers at Y

-> Extra: if you want the bunker be cloaked (completly cloaked, so you either can't see the graphic) you should add this:
Action: Remove 1 FLeetbeacon for PLAYER at X
Action: Move all Bunker for PLAYER at Y to X

NOTE: to do the extra you need a location (in this example X) with a 3x2 proporties, and in that location have to be around 50 fleetbeaocns
[50 fleetbeacons = 50 possible bunkers; 20 fleetbeacons = 20 possible bunkers and so on (for each fleetbeacon which was removed can a new bunker be moved to it)]

Hope that helps