I was just passing through this thread again and I noticed something I wrote in error:
i'm looking at a 2000 tacoma 4x4.
In general, I would recommend to try to get an engine that is as close to 1995 (if 4cyl) or 1996 (if V6) as possible, since this is the first year for OBD-II and will have the least amount of emissions related equipment (if applicable).
In California we have a smog law that prohibits installing an engine that is older than the vehicle it is being installed into.
In other words, if you have a year 2000 vehicle, then you may ONLY install an engine from a year 2000 vehicle or newer.
I don't know if this applies to you, but you might want to check it out first. If not, then definitely go with an engine that has less smog emissions if possible and practical.
BigMike