Sorry to bring back a dead thread, but I had to offer my opinion, and I feel the 2.8 is still a relevant topic in terms of engine swaps...
The 2.8 is showing itself to be a fantastic motor, but being a aftermarket-only option there is not currently a "junkyard" option for these motors, and this puts the cost of install out of reach for 75% of the public. for $9,000 just to get the motor, its a motor swap that can end up costing more than the vehicle it went in ($20-25k to have a shop put it in, and it may have only been a 15k vehicle to start with...)
As for the Chevy 350, it depends on the vehicle condition, budget and expectations of power.
1955 age comment?, are we forgetting the Toyota F engine is based off 1939 GMC designs? putting a date on a design isn't relevant to its effectiveness. If reliability and parts availability is a consideration, I would rather use an engine that has was used in production cars for 45 years, and continues to be available brand new from the manufacturer as well as the aftermarket. There is not a motor you can put in a FJ (or really in ANYTHING that has enough room) for less HP/$.
While there are huge benefits of EFI, and the LS (or Gen 3) chevy engines are miles ahead in terms of tech, I think it should also go without saying that there is nothing nostalgic about a LS engine, or even a modern cummins. Original or not, a period correct 350 can look right at home in a 70's cruiser.
ALL THAT being said, I have my original F engine in my cruiser and hope to keep it there. IF i was going to do any motor swap (other than a 2F) it would be a small block chevy 305 or 350, probably keep it carbureted but MAYBE a simple low cost TBI install. I enjoy the old character of these FJ40's, and thats why I own one. for me, the character is also in the old simple mechanics, not the miles of wiring to control individual coil packs for each cylinder...