uh . first off lol
the engines are the same other than turbo intake and intercooler.
the holes you have to plug? well after you install the engine i guess it would be the ones leaking some sort of fluid.
if you get a newer sti ngine with dual avcs you wont be able to control the exhaust and pray your intake cams are similar otherwise you will have lots of problems.
have you thought about the more common buick v6 engine swap?
Now that's thinking out of the boxer
fyi all 05 + legacy's have built in code reader