To verify they are PI heads you are going to have to yank the intake. If your intake holes are round you have NPI, if they are squarish you have PI heads. 13 bolts=Windsor but there were both NPI and PI Windsors.
Since the car is a 99 and you have a 6 bolt crank... my guess is that you have the original 99 PI heads/cams/intake and a NPI bottom end. Which would be a good thing as a PI swapped NPI is actually going to make a little more power than a regular PI motor, but you have to be aware of a few things if that is the case like a higher compression and a limited cam selection.
Only way to be totally sure what bottom end it is is to pull the heads unfortunately unless you can verify it from the previous owner along with what heads you have.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.