Quite a few things (mechanically) that can cause a fuel injected car to run poorly and the answer is usually pointed to by looking at when the symptom occurs.

But in your case, it sounds like the poor idle after starting is now happening both cold and hot. Of course you'll want to check for things like:
1) spark plug condition, gap and type (no platinums!)
2) spark plug and coil wire condition
3) distributor and rotor condition
4) air filter condition
5) fuel filter condition

And then move toward more complex causes, like:
6) Vacuum leaks into the intake
7) One way check valves in the fuel system that are bleeding off fuel pressure when the engine is shut off
8) Injector spray pattern
9) Control pressure regulator function
10) Any sort of auxilary air regulator's function

If it were mine, I'd run through the first group, and then go dump a can of SeaFoam, Lubromoly, or BG44K(the best) fuel injection cleaner in the tank and get out on the 5 freeway and run down to Stockton and back. And I'd recommend using only 91 octane at all times.

If the problem continues, dig into the second list.

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