My continued thanks to members of this forum for all the good information so far.
I filled my empty transmission with transmission fluid and then discovered that it was in fact my differential fluid I had mistook as transmission fluid, thanks to who I now regard as a less than competent mechanic who hates Subarus.
So I emptied the differential fluid, which came out black. I refilled with 80-90w gear oil. The car indeed seemed to improve. It no longer violently jerks, now it's been reduced to a relatively benign (but still concerning) clank. Here's the story:
When cold and driven up to 30 mph it is perfectly fine. After it warms up a bit there is a moderate clanking when acceleration is relieved. At highway speeds the clanking gets worse. You can feel it in the steering wheel and the shifter especially. The funny thing is it only happens when the throttle is nearly completely let off. If I put my foot down just enough to get throttle there is no clanking. I'm actually able to avoid the clanking entirely by applying a gently bit of acceleration as I brake. There is usually no clanking at all below 25 MPH even after a highway trip. It seems to occur at any RPM, speed, or gear. Possibly the first gear doesn't have this problem, I haven't tested that enough to be sure.
There is certainly a problem in the left front axle at the joint that's closer to the center. After a trip it is dripping grease onto the exhaust, causing a decent amount of smoke.
Is this a transmission problem? Or am I lucky enough that it all comes down to the axle? When I bought the car I was told the left bearing was about to go, which I have already replaced. Perhaps it was the axle problem and the previous owner was mistaken about it being the bearing?