The main issue is cost. I thought I got a good deal with a 3rd gen low mileage 3rz and all the accessories with it, but I had to change the harness and the computer to get it to pass California smog (and I still haven't ran it by a smog ref yet so there is no guarantees it will pass). I will also have to pay to have the exhaust re-routed since the smog laws changed this year.
Is that because your donor wasn't a California vehicle?