Flywheel, Clutch plate/disc, I'd imagine clutch fork and pin, throw out bearing, slave and master cylinders (might not be needed, but good to do anyway), and I'm not sure about the starter? Someone here will be able to confirm that. Tail shaft, rear diff, rear half shafts, front half shafts, cross member(s) for the trans.
Definitely will need the shifter linkage too. I used to own a S401, and that had the shifter linkage from a V7 WRX STI in it - so that's probably the way to go. I'd highly advise getting the Raceseng R-Lock reverse lockout to replace the factory plastic one while you're there too - won't rattle, and a much nicer piece being alloy! And also new shifter bushings too - preferably Delrin POM-C ones in my opinion.
Some of this stuff you may not need, due to Subaru's having heaps of interchangeable parts - why they're great!
But as stated about, multiple threads about this conversion.
Probably the best way to get a 6 speed box is to see if you can get first dibs on a BL/BP Legacy with the EZ30 and a 6 speed in a wreckers - especially a Pick-A-Part, as they charge a flat fee for a transmission.