As far as the engine, I'd be more concerned about the harness than the engine itself. Unless you really want the hydro fan, I wouldn't spend a bunch of time getting the whole motor changed just for that. The electronics are what you should be really worried about. There's a few differences here and there but a 1J is a 1J is a 1J once you take off the harness and other electronics.
I'd be worried about getting a Supra harness and ECU than getting an engine with a hydro fan on it. You can find a 1JZ engine all day long. The electronics are what's starting to become hard to come by.
But if you bought what was supposed to be a Supra motor set, you should have all the Supra related parts anyway to be satisfied...