Mustang Boards - What should I do?

It all depends on what your ultimate goal is. Remember that it's not as simple as supercharging it. The T45 only handle 330 ft-lbs torque, and your rear only has 28 spline axles. This should be fine provided that you don't load the drivetrain such that you reach the limits (easy to do w/ street tires, though one nasty clutch drop...). All too often supercharging is the first objective vs. the final goal. I myself have slowly been prepping my car for a 5.4 (between saving up the cash and rebuilding the rear end to handle my goals). If you are looking for cheap power that doesn't waste money, the PI swap is probably most cost effective. You get the better heads and intake which open up the flow and a nice boost in compression. If a supercharger is the final goal, new pistons to lower the compression would be needed anyway so raising the compression now with these heads don't make the heads a waste. Plus later on, if you want to upgrade the heads, your only options are PI style anyway (between aftermarket intakes and heads, unless you factor in porting). A CAI though, is a waste. Headers though are magnificent. I still miss my old Hooker headers (even with 3.73s, I still miss them) but they are a PITA to install AND maintain. A good header goes a long way to help with these two, but regardless, the tight space involved may be too much for you. Shorties on the hand are worthless unless you are pushing a lot of air through the engine, so those would be best saved for once you decide to supercharge.

In short, do the PI swap. You'll make a nice gain in power w/o needing to spend a ton more to make the drivetrain and other components handle it. Plus it gives you a nice base to work from for later upgrades.