There are a few reasons to do what you are looking to do.
1. You want to keep your stock stuff free from rash if you crash.
2. You want to go fast and the Mille Fairing is good for another 3mph on the top end
3. You are a Newbie to track days and you want to win the award for Biggest NOOB.
Just bring your bike with good tires and brakes and follow the track day rules for safety wiring. Spend your money on good leathers, boots and helmet that fits right and not loose as riding at track speeds with a loose helmet is a real pain.
If you crash you will be surprised how easily the bike will turn leprous even with all the frame savers you can buy on it. Do yourself a favor and just go and have fun. Don't ride over your head and crash. If you want to go faster and you plan on pushing the limit then go out and get a crashed bike from some salvage yard that still runs and is straight for about the same amount of money you can buy Mille bodywork for. Of find the local club racing web site and purchase an old race bike that isn't competative any longer (older R6's and GSXR600's) and pick up something like that for track day only fun. You'll end up saving money in the long run crashing one of those than your street bike.
I now take my Buell XB12R to the track and ride it at about 80% my old race pace and have a safe fun time. I will keep doing this as long as I can fit into my Vanson's.
I don't know about the mille. What I do know is that air-tech makes race bodywork for your falco. call them and ask. i bet the mille doesn't work or they would not make specific stuff, but that's not always true for example i ran old tlr race bodywork on an sv racebike and it workled fine with a little modification.
your powercommander question is more complicated. if you have snatchy throttle anywhere on the pickup, you might be abe to use it right away. but the best way to avail yourself of a power commander is to have it mapped for the track your at, by someone with a dyno and an exhaust sniffer. the maps you get with the machine or download are fine but not perfect and thats the whole point of a power commander in my view.
On my Suzukis I just have the stock box tweaked with a teka tool and a sniffer and it works great.
have a great time. and remember its important at first to go slow so you can go fast later.
in summary i doubt a power commander will do you all that much good unless the falco is like to sp1 Honda rc51 which realy needed one.
I don't know. I do have a fairing lower and stock clip-ons for a Falco. I bought the lower from the Aprilia forum and the clip-ons are leftover after I installed Heli Bars. The Falco is gone and I have no need for the stuff. my email is [email protected] if interested. J