Depends, is it a Lincoln Continental with a FWD 4.6L DOHC or a Mark 8 RWD?
If it's FWD, not too much really. The FWD block won't mount in RWD applications.
If it's a Mark 8, it can be made to work, but you should prob do a lot of research first. It's not a 100% direct swap but it can be done. Your stock trans won't bolt up either
On top of all that, you have to think about the laws in your area and what you can get away with, the 99 mustang model has to conform with having a V6 engine and complete hardware that goes with it (catalytics, emmision standards, etc)