I am currently doing the same thing, I have both engines pulled. This is what I have found so far, the down pipe for the exhaust is different the 3.1 mount to the manifold the both holes are at an angle where as the 3.8 is at 3 and 9 positions. The exhaust need to come from the 3.8 car as the SE only has one muffler. The AC compressor and lines will need to be used from the 3.8 as the 3.1 is different. The power steering lines will need to be modified some as the 3.1 pump is located on the top of the engine. The hoses can not me changed as the lines mount in different locations on the rack and pinion.
The fuel lines need to come from the S/C car and grafted to the new body as the SE 3.1 end in a different location. Need the fuel pump out of the 3.8 car to the SE I am not sure about the wiring to the fuel pump as I have not got that far yet. The air box, computer, overflow tank and radiator needs to be from the 3.8.
The wiring I have not compared the engine bay fuse box yet but this needs to be done so you do not burn something up.
The trans will bolt up to the 3.8 but I have been told the 3.1 trans will not last long if you keep your foot in it alot as the 3.8 S/C has a HD trans.
Good luck hope all goes well I will be dropping the 3.8 into the SE this weekend I will let you know anything else I run into.
