no there shouldn't be. but there can be little things like abs and cruiz control that could be different, the the bulk should be the same. the easiest and most sure proof way is to unplug all your harness from your engine, pull the motor, then put the new one in and hook it to your original harness. then if it is a little bit different you can swap the parts needed (which i doubt) but it would be good to keep your original harness and computer. also you have to remember that 4runners have a more complicate harness are different. so unless this engine is coming from a 99runner same model then i would definitely just use the new engine and block and head and then use everything else from the original engine. thats jsut a sure proof way. that way you dont run into problems later down the road.
i have dealt with this same thing but it was on a 22re, i got an engine from a truck and tried to put it in the runner using the other engine harness and didn't work out to well. but it was a learning experience. ended up just using my original harness, intake, fuel rail. and putting in the long block assembly from the new working engine.
either way is was really simple and didn't take much time to swap everything.
