Okay, hope this helps you:
Your Wagon has the same engine bay as a LX, so this could help alot of you.
The BP(D) 1.8, is actually the motor in our GT´s, You mentioned an intercooler so I´m guessing you mean the GTX motor (mazda BPT .
Either way both motors from the outside look the same, except for the turbo and intercooler. And to answer your turbo question simply I would *HIGHLY* recommend intercooling. Even the GTX´s came stock with an intercooler. Not only does it put a few more horses down, colder air helps your engine last longer and just makes a lot of hard work seem worth it.
Okay, your other question was about the tranny.....no your tranny will not work. Yes a tranny from an EGT would work because its the same motor(essentially).
Now here´s your prob....The 1.9L and the 1.8L dont sit the same in the scorts. So, for you to drop a 1.8 you´d be looking at pulling everything out of your LX. Your motor, tranny, half shafts --->all the way to CV´s, rack and pinion actually sits a little different too. Once the everything shy of struts and springs and balljoints are gone, you´d have to pull the engine mounts and get GT ones. Then figure out a way to get them mounted.
From there you´re entire project will be custom fabrication. And then, like myself, you´d get all the parts stores telling you "there´s no listing for the parts your asking about," or like the way the Ford dealership told me there´s no way to turbo an escort.
But,.... if you could get the engine swap in, bolting a turbo the EGT motor would be your easiest task. Especially since your going to have to get a new ECU and wiring harness for the engine swap you might as well just get a Haltech and that will take care of your fuel map, ignition advance and retard, boost control, and all the little things that are annoying when just turbo´ing an EGT.