00 to 01 engine swap question

[snagss]

Here is the deal. I have a 2000 stang that was rolled, engine still good, as a matter of fact I drove the 2000 to the spot where I pulled the engine. I also bought a 2001 stang with what the owner said “internal engine problems”. I notice the oil mix with water (possible blown head gasket) to start with. Decided that I was not going to mess with the 01 engine and took both engines out. Placed the 00 engine in the 01 body and notice that some of the connectors on the wiring harness will not fit, i.e. alternator, EGR, knock sensor, coil pack and some sending units. I replaced all the part on the good engine for the parts from the 01 except for the wheel that is next to the balancer which gives the information to knock sensor. Engine starts and runs smooth, but I have a clacking noise. I was told that the knock sensor and balancer are compatible so i am sticking with the 2000. Also was told to change from the lower intake manifold on up ( i just changed the upper so will do the rest this w-end) The $ ? is, what else do I need to change? I am just waiting for the rain to stop to get on this. And yes I alredy used the search button and couldn't find anything. Thanks for all positive answers.