The sm420 that I bought was 2wd, so there wasn't a tcase attached to it. I personally don't even know what is available to bolt up to it. Anyways- I bought an adaptor, and kept my three speed tcase, mainly because I didn't want to mess with the offset diffs. But for the cost of an adaptor (mine was like $350 a couple years ago), I probably could have picked up a GM tcase and a centered rear output for not too much more. But then when you look into which rear axle to run, things to consider: you have to find a diff with the right gearing, 1/2ton axles have the same bolt pattern as cruisers, but the beefier 3/4ton axles have 8 lug wheels, you will need to run new brake lines with standard fittings, and adaptors where necessary, you will no longer have the parking brake on the rear of the tcase so you'll have to rig an e-brake up with the rear drums or something, and you'll need some driveshafts with the right flanges for the tcase and diff, and driveshaft length is an issue in the fj40's that don't have much room behind the tcase...
Drawbacks from keeping the cruiser tcase are: aluminum housing, breakage-prone nose cone, adaptor clocking issues, grinding on the sm420 for the front output flange. Stuff like that.
If you forsee yourself upgrading your axles in the future, then just get it over with, and do it now. Read plenty of articles in the tech section before you do anything else. But if you're going to be running 35's or smaller, the stock axles should be fine (assuming that you're not a maniac with the gas pedal). I am going to run my 3spd tcase until I have the time and money for a 203/205 doubler. Which will probably be a while, but I'm not worried about the case. Keep fluids in them, and they'll run forever.
Anyways- hope that helps. Best of luck on the swap!
Zipp.