There is a bunch of info out there on the different versions of the 4.6L motor from the two plants that make it... I think, all told, there are about 20 different versions of the 4.6L block... I just did an 8 bolt 97 Windsor motor to 6 bolt 2001 Romeo motor swap... I have a "pinging" problem, but I think that is associated to my use of flat-top pistons, not the motor in stock form... I used my 97 wiring with the 01 motor, which could also be my issue, but again that isn't associated to the "motor" itself...
So, yes... I am fairly confident that it will work without too many issues...