Suspension wise the intrepid R/T only had a stiffer spring rate, same shocks and sway bars.
Performance wise the R/T had a different intake manifold and PCM.
Suspension wise 300M special had stiffer struts and springs, bigger swaybars and wider tires.
Performance same deal, except the PCM was supposed to bascially max out the performance of the 3.5L.
For example, my 3.5 non-HO ran a 16.4 stock with 16" wheels.
Had the swap done (300M special), used a K&N FIPK and threw on 18" wheels. Car ran a 16.2. However, he previous car I had was a 3.2L Concorde and that ran a 16.7 with the same wheels. That's a half second difference thanks to intake/programming (both cars ran the same stock), mostly due to changing the peak torque lower (4krpm vs 5k for non-HO).
It is a pain though as paintballdude mentioned that you will need a DRBIII or a dealer to program.
And lastly, you can ONLY do this for cars made from 2002-2004. If you have a 3.5L before that then it already a HO unit.