The S14 engine harness will have more plugs than the S13 has to plug into. There are certain imcompatable items, for instance your temp gauge may not read properly because the S13 and S14 temp sensors give off different signals. Others like the speedsensor may need to be changed to an S13 sensor.
There are 3 generations of S14 SR20DET's. The only real differences between them is that the wiring is changed slightly. The early model uses an ECU that has a red WC symbol on it. Middle gen has a black WC symbol on it. The latest gen has a NA symbol on it.
The WC's shouldnt be terrible hard to install if you use the S14 SR20DET FSM available here:
http://www.zeroyon.com/TheSite/techservice.html
The wiring for the last gen engine with the NA ecu isn't readily available. My friend has a late model S14 SR, we just used the entire harness off the clip rather than trying to figure out the wiring.
The wiring will be the only major issue, the engine should drop in just fine without clearance issues.