The FJ60 bellhousing will work, but you will need to fabricate a cross member. The early FJ40 4-speed bellhousings have dog-ear engine mounts that attach to the frame. The FJ60's do not.
You should be a little carefull here. The early FJ60 bellhouses were inline with the FJ40 4 spd ones, at least in late production. The mid-production FJ60 used a "3F" bellhouse thaet canted the tranny 7 degrees toward the NA diver's side IIRC. This allowed for the use of a "normal" front drive set-up without double cardigan and for room for the spacer where the H42's 5th gear should have been.
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