Do you have a standard Ford starter relay like the original style? Or a more modern one that only has the small "S" terminal but not the "I" terminal?
Got pics of under the hood in that area?
Where is the White FiTech wire coming from? Directly from the ignition switch, or somewhere else?
Are you using a ballast resistor in this ignition setup? You should not be, so I wanted to make sure.
Things you can test easily with a volt/ohm meter:
1. If you have the Brown "I" wire connected to the starter relay, pull it off and measure voltage with the key in RUN. If it is not powered there is a break in the circuit somewhere.
In theory you no longer need this Brown wire anyway, since you are running an MSD setup that takes the full 12v of your system. But it should not hurt anything to keep it in place, as long as the starter relay is not shorting it out somehow.
2. From the back of the ignition switch, or up at the ignition box you will have a Red w/green stripe wire. Should have battery voltage in RUN, but should also have it in START, which it sounds like you don't have. However, you should test that theory anyway.
With both the Red w/blue "S" wire and the Brown "I" wire disconnected from the starter relay so the starter does not crank and you don't get a false signal to the other wires, have a helper turn the key to START while you test for full voltage at the Red w/green ignition wire. If power is present at RUN, but it goes away in START, your ignition switch is bad.
Remember, "new" does not mean "good" anymore.
And if any of those voltage readings you are taking are less than they should be, find out why. Even with all that wire, this new Painless system should have very minimal voltage drops along it's length.
If you find more than a half-volt drop anywhere, find out why.
Good luck.
Paul