Can you put an 03' Mustang Cobra supercharger on a 99' Mustang Cobra?
If all you want is the power increase then it would probably make a little more sense to put a centrifugal supercharger on it instead of a roots or screw type supercharger. The installation will be MUCH easier. If you are set on the 03-04 supercharger, it can be done but will cost you a lot more and the installation will be more difficult. The only down side to the centrifugal supercharger is that it will not produce as much boost at lower RPM's but plenty of power can still be made. I personally would hesitate to add forced induction to an engine with 90,000 miles on it but that is up to you. Can the engine handle it?--maybe but for how long is the question I would be worried about. Maybe freshen up the bottom with a hone or light bore if necessary, new bearings, piston rings etc.
To add to an above post, you will not need the entire engine. The 99's bottom end is forged and (assuming reasonable mileage) will handle the boost