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.