Question is we just bought an 1997 F150 with the 4.6 Romeo in it, we need to find a new engine and are trying to figure out what all has to be changed in order to use the 4.6 Romeo out of a 1999 F150? Also does anyone know what has to be changed in order to use the engine from a Crown Vic?

 

The '99 basic engine should fit, but there may be changes in sensors and accessories. Ford modulars don't necessarily interchange from model year to model year.
Get down and dirty and search the replacement parts lists for both engines and see how they compare.
You will need to keep all accessories from the '97 in order to make the '99 comply with the onboard electronics of the '97.....the ignition systems are probably different: EDIS-8 for the '97 and probably COP for the '99 for example.
Follow the same routine for any replacement candidate, Crown Vic or otherwise.
Here's some good info that may help with your project:
http://en.wikipedia.org/wiki/Ford_Modular_engine
Note: The Romeo and Windsor engines are very different. Don't try to mix and match.