yea, you'll need the harness and ecu since your going from obdI to obd II. i dont see why not, if you can got form new to old, y not old to new. just make sure you use all the mounts and everything from the 2000 block, like alt bracket, ps bracket. you might have to use the engine mounts from your, 86 though, im not 100% on this though.
whatd you blow on the old engine, it might actually be easier in the long run to just repair the 86, then you can do a complete build on the '00, unless you already built the '00 engine, like rods, pistons, etc.