The direct ignition coil pack sits over 3 plugs and that's where wires lead from and to the other 3 spark plugs. The system you knew before was distributed spark with a distributor and wires that led from the distributor cap to the spark plugs.
Have you pulled yer plugs and looked at the condition of them? Did you pull any codes from yer ECU via the OBDII port? You could buy and use some of the newer diagnostic setups that you can run from yer computer to yer vehicle to actually see what part isn't doing their job.
AutoTap is one... You can also drop by AutoZone and have them pull the codes fer you.
Keep in mind that the ECU (computer) controls just about everything dealing with the operation of the engine based on the various sensors littered about. If a sensor should go wrong...well...I'm sure you can see where that could lead to bad performance. I'm thinking that yer coolant temp sensor could be bad as this seems a common part to fail and cause problems. You can search fer posts in reference to that and you should be able to find the proper resistance value fer it at temp.
