The TSB for the valve cover and upper intake manifold bolts / gaskets is for '99 and newer. They started using a different intake manifold in '99 that was causing problems. This TSB does NOT apply to your '98.
Cleaning EGR ports is standard....normal service at the age / miles.
Vaccum leaks are an issue on almost any car.....and can be hard to track down.
Check the elbow that is on the top of the upper intake manifold......next to the throttle body. The Elbow points toward the firewall.....and goes to the PCV valve. They can develop a crack on the inside of the elbow.
Also, check to make sure that the dip stick is fully seated. The air that flows into the front valve cover to replace the air that the PCV takes out....is measured.....flows through the MAF with the rest of the air. So....if the dip stick is not seated fully.....air can leak in......which the computer does not know about.
Make sure that the red vaccum line that connects to the fuel pressure regulator is correctly seated. The fuel pressure regulator is mounted to the crome fuel rail.....on the passenger side. The red vaccum line connects to the top of it.
Double check to make sure that no vaccum lines have been bumped loose... There are a bunch of them on the back side of the upper intake manifold......back where you cannot see them....so you have to feel around back there.
I have a number of pictures of my '96 3.8L....that may help you find things....as your '98 will be very similar.
http://community.webshots.com/album/201931518cScpNK