Extremely tall ask, especially for someone asking such basic questions. I'll slide my bet onto "this project never happens".
You have a big list of things there, it's not going to happen quickly. I'd guess multiple hundreds of hours of labor to complete that list. Maybe with hundreds of hours of research/parts gathering, you could have the car out of commission for one hundred hours of work time.
However you slice it, that's an enormous amount of labor to bring it up to 30 year old technology. The early EJ22s are reliable and fairly simple, but not fast. If your target is a long travel thing like the Subaru version of Caswell's Baja Pig. You'll be looking at turbo platforms, or H6s, or both. You'll need a better transmission and rear diff. And custom suspension and axles. All of which means any work you do with the Legacy parts will get you no closer, and have to be completely un-/re-done.
Sure, swap the engine/transmission. Keep the suspension stock and serviceable. And it'll be a fun, reliable little street car.
If you want to offroad it, get a D/R 5MT to go behind the EJ22, redrill the hubs to 6-lug and a 4" lift. And you'll have a fun, reliable little wheeler.
If you want any more than that, you're starting with a rough platform, and definitely have the wrong donor to get there.
Really think what your budget (money AND time) is, and what your goals are.