Generally speaking, the engine has to come from the same model year or newer. You also have to have all the emissions equipment in place that came with the NEW engine. That means for guys who swap 3.4 into a truck with a 3.0 you'd have to have all 4 catalytic converters, not just the 2 the 3.0 had. You asked if a 350 is legal, yes, and I think you should put all the emissions stuff in. I hate sitting behind a vehicle in a traffic jam or drive thru that is just spewing all that nasty exhaust. Not to mention my kids have asthma as it is.

94 SR5 4-Runner
167000 Miles and going strong
BJ Spacers, Fj80 coils, MT/R's
Lock Right front and rear