I really don't see any reason to change anything on the base engine at all. One may have a balance shaft in it, and the other not, but that wont affect it's operation. The engines, for all intents and purposes, are the same. The difference will be in the engine controls. You will have to swap the sensors and wiring harness. The engine control stuff needs to stay with their respective vehicles, because that is definitely different, since one is OBD1 and the other is OBD2. Use only the base engine, and you should be fine, as long as the bellhousing is the same.
Changing head bolts is never a necessity, unless you have an issue with bolts breaking etc.
The 2005 Ford Taurus has 40 in. of front head room.
The 2004 Ford Taurus has 40 in. of front head room.
The 2011 Ford Taurus has 39.0 in. of front head room.
The 2001 Ford Taurus has 38.1 in. of rear head room.
The 2005 Ford Taurus has 38.1 in. of rear head room.
The 2004 Ford Taurus has 38.1 in. of rear head room.
The 2008 Ford Taurus has 38.8 in. of rear head room.
The 2014 Ford Taurus has 39.0 in. of front head room.
The 2003 Ford Taurus has 40 in. of front head room.
The 2012 Ford Taurus has 37.8 in. of rear head room.
The 2007 Ford Taurus has 40.0 in. of front head room.