Welcome aboard Michael!!!
The Power Commander 5 and the MSD will function fairly similarly as far as fuel goes... When that day comes you want to start playing with the ignition timing, this is where the MSD will shine as it serves as a dual purpose controller (fuel and ignition). The problem with the MSD that I've seen is that the fuel maps/ignition maps seem to be far and between where as for the Power Commander they are readily available (both 3 and 5 versions.. if It's PC3, it is easily convertible to be used on the 5).
Onto Intakes.
you really can't go wrong with any intake. If you're just doing the "big 3" Intake, Exhaust, and fuel controller. It depends on where you "think" you'll be going next as far as mods go.. If you go into the motor (Port/high comp piston, cam.. etc) it may be best to plan ahead and go the FCI route, as that seems to have the most flow right now. If you don't plan on going in, you cant really go wrong with any of the options you listed. Monster, Trinity, or Pro-Design.
