My 98 LX is in the shop right now for the same issues. My car needs 2 oxygen sensors, both upper and lower intake manifold gaskets and a new fuel filter. I'm also having plugs and wires put in as well. So, if the things you've fixed aren't the problem, definetely check your LIM/UIM gaskets.
Also, this is my best friends auto shop so I know he isn't railing me on the work or saying there are extra problems and unlike the dealer, I'm there when he does the work and can see the diagnostics myself.
So again, if the problems you're fixing don't ultimately fix the BIG issues, check for vac leaks and the LIM/UIM gaskets..