First off, virtually ANY engine can fit ANY car with enough effort and $$$$.
Second, here's a link to the StangNet V6 forum: 94-04 V6 Mustang - V6 Tech at StangNet
You want an easy way to check if the intake manifolds will swap without doing a damn thing ? Go to your favorite parts supplier and have the pull a set of intake manifold gaskets out for both year motors..... infact you can look them up online from your chair and see if they are the same part number. If they are the same part number you are good to go. If not that doesn't mean they don't interchange, there just may be slight differences and it could still fit.