Scratch that....you shouldn't need to change the cylinder heads. Although the ports will be a little mismatched, you should easily be able to solve the issue with a couple of strategically placed dabs of RVT silicone, or if you're really concerned a set of NPI to PI adapter plates.
What you probably will need though, is the timing cover from a later model PI engine. Although I'm not certain of this, I believe some of the accessory placement changed between the early NPI cars and the later PI cars.
You'll probably also need to fabricate some sort of custom brackets for your coil packs, since the Series IV was built for a '99-'04 Mustang, that utilizes a COP (Coil on Plug) ignition set up. The need for custom fuel rails may also arise, since yours are based on the return style set up and the later PI cars are not.
Finally...I would skip replacing the 30lb/hr injectors with another set and go right to a set of 42lb/hr units. The 30's will be running on their ragged edge with that blower, especially if you deviate from the stock boost levels.
Any way you slice it, $3,000 isn’t a bad price for the kit assuming its complete other than the injectors.