I am new to the SuperCharger engines,but mine has an A&A Vortec SuperCharger on a LS3 engine and has a intercooler.Even if a intercooler was not needed I think I would run one to be on the safe side.I would read the instructions and try to follow them as close as possible.
As for the 4-speed manual trans it will work great and be a blast driving it on the street.Mine has a manual 6 speed and for street driving an maybe a little track time & street racing there is no way I would change it over to a Automatic.
I would use all MSD dist.,coil & MSD box with the upgrade as well.And after you get it going the only thing left you will need is a set of DOT Drag Radials!