There should be no differences, possibly EGR however? Someone like dapepper could probably answer that.
A good port and polish job would be great if you have the time and since you got them for free.
Check out this thread on modding the intake
You can polish the intake runners for better flow. On the throttle body you can cut off the rings that sit around the butterflies and polish the surface where the air flows into the holes.
Good thread about that here
All in all you could
1. Modify, port and polish the "keg" style intake
2. Modify and polish the throttle body
3. Do the plenum fix (check the stickied thread) since you'll have the intake off
4. Add some inexpensive headers like pacesetters
5. Add some roller rockers
6. Replace the intake and throttle body gaskets
And you'd have a great setup for only about $800 or less depending
If you do not add the supporting mods and just modify the intake and TB, I woulden't expect the notice a change because the Keg intake isn't
that bad at airflow.
Since you already have the tools and extra parts, this could be a worthwhile build without a ton of work and $