I have 99 shocks on mine, and they fit without any problems.
The 99 Struts should work too, but keep in mind they have a lower spindle mounting location for the newer stangs. If your not lowered you should be fine, but if you are lowered, you may bottom out.
I'm just going off what I know. A side by side comparison show a definate length difference between the two, due to the spindles lower mounting location. There is a good chance that the strut could bottom out, possibly damaging itself and/or something else. It's up to you though.