If you REALLY are daft enough to pull a perfectly good TT engine out and drop in an N/A (you'll have no trouble finding a buyer!), I say just drop the N/A in and start her up. Drive her. If you get CEL's popping up, go from there.
You'll likely have to find an N/A ECU for it, it's just a matter of finding one that plugs in. Start by researching if 98-00 N/A's have the 4/3-Plug setup (Phase 2's have a 4 socket ECU, but only 3 loom plugs are used). If they do, you're in luck, and chances are wiring will be essentially the same. At least, this is the case for the 96-98 era.
Engine wise, you're better off keeping the TT engine loom and swaping it onto the N/A. I think doing this should avoid future wiring f***ups. At the ECU end, you may have to change it to wasted spark though, as most subaru N/A's from the era are indeed wasted spark, and so their ECU's will only have 2 ignition outputs. Don't worry, Coil-on-plug can be run as wasted spark (though they will simply age twice as quick)
As for the ECU, any N/A ECU can dive any N/A of the same era. SOHC, DOHC, doesn't matter, YEAR is what matters (timing marks, sensors etc). We have run SOHC's on DOHC ecu's before. Only thing to watch out for is the injectors, 2.2's should be run on red tops. DOHC's have red tops, so are a good start. 2L SOHCs run whites, which flow less, so you might have lean issues at the redline in that case. (Again, a disclaimer here, this is talking from my 96-98 era knowledge, things may have changed dramatically for post 98, and my only post 98 knowledge is of turbo shit)
Also to note, 98 is when subaru introduced AVCS, which adds a whole clusterf*** of f***ery, SO AVOID THESE ENGINES AND ECU's, They will just unleash a world of pain and misery upon you.
Where to start for you? Start with the BH TX's. IIRC, they will have a 2L SOHC, so won't have AVCS. Find out what injectors they run, find out what type of ECU they use. Also try and find out if they made a 2L DOHC without AVCS. If so, you def want and ECU from one of them (will likely drive more appropriate injectors)
At the end of the day, I think you're mad for doing this, but if you want to, just PM me, I'm happy to help out fellow subie owners when I can.