What year SVT engine?
The things that make the SVT engine different fron the non SVT engine are intake manifolds, throttle body, cams, head porting, slightly higher compression from different pistons, bigger injectors, and different PCM controls.
98's only had the secondary intake ports ported via extrude hone process while the 99 and newer had both primary and secondary ports ported.
If you don't use the cams, you won't be getting a lot of the improvement that the additional airflow from the better intake stuff will provide.
The slight compression increase is not enough to worry about.
If you use the 19 lb injectors from the SVT you will need to do something to compensate for the larger flow. If you don't, you may be running a bit lean under heavy load. Some have used the SVT intake stuff with the non SVT injectors with no real problems.
Additional head proting can be very beneficial as long as you have someone do it that knows what he is doing.
With the increases in intake flow, don't forget to open up the exhaust too.
Depending on what year the two engines are, you may have trouble using the SVT cams. I don't remember when the change was made, but later 2.5 Duratec engines (both SVT and non SVT) used narrower timing chains with narrower cam sprockets. You must make sure that they are compatable.
The SVT trans and the non SVT MTX is the same although the SVT has a better clutch and a lighter flywheel.
You should be able to learn a lot more about your porject by searching around these forums.
Good luck, it all sounds like fun.