If I were you, I would replace all four spark plugs and go buy one used or aftermarket coil. Change the spark plugs, and if it still runs rough, swap the new coil in each spark plug until you've done all four. These coils are much cheaper on ebay (MUCH CHEAPER). If the problem persists, wiggle the wiring at each coil - one by one (make sure you don't also wiggle the other coils wiring). If you find one makes it better, then you can re-crimp the wiring in that connector and see if that helps. You could also go buy a used coil connector (with wires still attached) from an auto-wrecker, and swap it for the one that you determine has a bad connection.
If none of this helps, try unplugging and replugging (one by one) every connector you can find on the engine so they are all re-seated. You can also pull gently on each wire that goes into each connector to see if one pulls out. If it does, that was likely a bad connection. If you are very careful, you should be able to remove just that one pin and solder the wire to it, then replace it in the connector. If you don't think your up to doing that connector soldering stuff, find the bad connection then have a stereo shop repair the connection.
If I had a wiring diagram for your car, I could help more, but Toyota is very stingy with that information and it's not widely available at a DIY budget.
Hope this helps you. If it does, please post so others know what fixed it in case they have a similar problem.
Regards,
Dale
