ls1killer, we ran into this problem a week ago. We went by the VIN number when we were ordering engine parts. When it came time to bolt the valve covers on, we opened the box, and we had the wrong ones. The VIN said it should have had a Windsor engine, but in reality, it had a Romeo. The car was an 01 GT.
Easiest thing to do is just count the valve cover bolts.
mustangman98, the valve covers that Chad sells are nice. Those are the ones we ended up going with on the 01 GT we worked on.