86.5 + GTE = swap... whether JDM or domestic. Seeing that there is an EGR modulator behind the intake plenum I am not inclined to believe this is a JDM engine... not that it matters; There was no power difference between the two.
I wouldn't worry about swapping anything at the moment, I'd focus on fixing what's broken first. With the exhaust, I'd wait on replacing any one given part until you can afford to just do it all. Otherwise you'll be replacing the 2.5" muffler with a 3" in a year when you upgrade the piping. Also, the stock resonator (like the stock muffler) is a baffled type and as such poses a good deal of restriction. I suggest replacing it with a harmonic resonator (helmholtz resonator); They're free flowing and smooth out the airflow.
Don't just leave the air filter in the engine bay. Add some pipe and extend it up under the headlight or build a box around it.
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