When I check
Toyota Parts and Accessories - Official Online Store, the Toyota part number ( 16410AZ011 ) for the radiator assembly is the same for both AT and MT on the 2000 SR-5s. Both trucks also share a frame and mounts AFAIK, so I doubt there's any difference in placement or clearance. (Somebody correct me if I'm wrong.)
Now the 4WD and 2WD trucks do not share a frame exactly, but I believe the only difference is the location of one of the crossmembers. So I don't think there would be any difference in placement or clearance regarding the radiator assembly. (Again, somebody chime in if this it not correct.)
Yes to this. It's relatively cheap to replace the radiator and you might as well do it during another job. Especially since our original radiators definitely do not last forever, and when they fail, it can be rather catastrophic.
Good luck!