What you can do to the 2.9 is this...
Get a MAF 3.0 computer and maf sensor from a taurus/ranger/aerostar, verify the pinout, but it should be the same, add a pigtail for the MAF sensor.
Send your cam to Delta camshaft and have them grind you up their RV grind and some new lifters.
Gasket match your lower intake to the head, and your upper intake to the lower intake, can easily be done with a dremel.
If I remember correctly, you can use the flat top pistons from a 2.8 in the 2.9 for a compression bump, however I could be wrong.
Dont waste your time porting the heads, chances are youll replace one in the future and you wont wanna go through the hassle of porting another head, plus the benefits are very little for the amount of work put into them. If you have the heads done, use 88tm castings or even better the world products castings. The 86tm heads have a VERY bad rep for cracking, the 88tm's crack too, but not as often.
You could have a machine shop turn you up some rocker arm spacers to get rid of the springs on the shafts, this will free up a couple of HP.
Get some headers on it, and make sure you have a nice free flowing cold air intake and thats just about all you can do short of boosting it.