You should still be able to get the boot CD if you have the necessary license and a current support contract, I think the latest available is 4.1 which should work for your 2003 server.
Otherwise you may have to look demoting the DC, and promoting a new server to DC which would allow you to do a hot clone just of your app server. Obviously, I dont know your environment etc and whether this is a valid approach for you.
There are other tools available that can help with P2V such as platespin etc, but not free.