Different engine, PCM (ECU, Computer, etc.), Mounts and all.
Great swap and I hope you can see it through, it would be awesome.
The FWD 3.8L block will bolt to a 3.0L trans (since the Taurus guys can swap and our blocks are the same), so the FWD 3.8L Block gets FWD heads, intake and SC. Invest lots of money in quality head gaskets and head studs.
Go for a T5 swap (see my site) since you are doing so much work.