Will porting the lower and middle intake manifolds on the 2.8 result in any worthwhile performance gain? What are the major restrictions in them? I have an extra set laying around that I was thinking about playing with. My plan is to eventually fabriate an upper plennum.

According to my Big Fiero Parts Book, the lower intake manifold is a major obstruction to airflow. Here is what they reccomend for it.
1- Using a die grinder, just radius out from the injector hole to the scribed line you have made on the head side-mounting surface. This will restore most of the cone shape pattern of the fuel injectors and increase airflow. The scribe lines are made by matching the gaskets to the intake and scribing their opening. You can do this for the heads also.
2- Remove the casting ridges just past the fuel injector holes.
3- Port match the remaining areas (not the areas by the injector holes), and blend this areas back 1/2 inch.
4- Repeat the marking procedures for the top of the intake manifold (where it joins the center intake) and carefully open and smooth these areas. Be careful, as these areas are very thin.
5- When cleaning and rinsing the lower intake manifold, take extra care and time in cleaning the cold start injector passages. There is one output hole per intake runner, which is about 3/16" in diameter. Make sure these holes are open and clean. Use brake cleaner or Gum Out to clean these passages.
6- Use FelPro Blue as a gasket sealant on both sides of the gaskets and follow the shop manual for torque sequence for tightening the intake to the head bolts.
Hope this helps.

I know this has been said a hundred times (101 now...) but if you do the heads too, don't grind down the "shark fin" that protrudes into the intake port, as this is actually of benefit to air flow. It's OK to smooth it up, but don't grind it out completely.