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1, the 98 is non vvti, so you would have to swap the head from the previous engine.
2 the 98/99 engines have a different offset for the crank position sensor wheel (toothed wheel inside the timing cover) this will need to be swapped to the 00-02 wheel.
other than those two things, the bottom end is the same. you would be using the 02's electronics so no you would not have to swap out the ecu. its a pretty straight forward swap. just toyota changed a few things to support the new vvti system and new coil on plug ignition system, which i listed above.
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