Here's what I'd do at this point. Start over with the basics and ignore the codes unless the engine light is on when it's running. In fact disconnect the battery neg cable for a minute or so to clear them. While your at it, take that negative battery cable that you disconnected and touch the battery positive post with it. What this does is fully discharges the ECM capacitors. It's mostly used for newer ECM's, but still worth doing on the older models too. Just a habit I got into when diagnosing driveabilty problems. If your not sure what I mean by touching the negative cable to the positive post, don't do it...I don't want you to short anything out or cause more problems than you have.
Spark...make sure you have plenty of it at the plug itself. Best bet is to use a spark tester, like a "ST125" or similar. Most auto parts store carry them. Be sure to check every wire while the engine is running. Shut the engine off each time you move the tester to another wire so you don't get zapped. The old screwdriver trick will work but it's not 100% foolproof, the ST125 is!! Look inside the dist cap for moisture, corrosion or carbon tracks. Just because it's fairly new, doesn't mean it's not the problem. Same with the rotor, is the tab in the center clean?
Fuel...put a gauge on it to verify pressure. I think it should be about 9-13 psi, but I'm not certain. Check the manual if you have one. Another thing you can check is the injector(s) in the throttle body when the engine is running...you might need a helper to assist in all the start ups so you can stay under the hood and check everything. Is there a good cone shaped spray pattern with no drips? If it has 2 injectors, make sure both are spraying the same.
Air intake and exhaust...remove the air filter, sometimes it's easily overlooked. Use a light to see if it's clean, but removing it will prove if it's the problem or not. If you haven't checked the exhaust back pressure yet, at least make sure you can feel a moderate amount of pressure coming out the tail pipe with the engine at about 2K rpm. Connect a vacuum gauge to a vacuum line or use a 'T' and see what you have for a reading at a constant rpm(I know it might be tough to get a steady rpm), and be sure the needle is steady and not fluttering...I believe this engine is known for eating camshafts?? A compression test might be useful too. If you can narrow the problem to a specific cyl it's worth checking after verifying spark and fuel, but hold off for now.
Running rich or lean...since you don't have a scan tool to read engine data, do this. First create a large vacuum leak, the brake booster or PCV hose will work. If it runs better, the vehicle is running rich(pressure regulator maybe?). Next disconnect the Map sensor if you know where it is. Pull the vacuum line from it or remove the sensor from the intake and plug the vacuum leak off. If it runs better, the vehicle is running lean. You could also unplug the coolant sensor for the ECM, but using the Map sensor is more accurate.
Last but not least...ECM or connection problems. If any sensor was at fault, most likely the check engine would be on with the engine running and a code would set. Locate the ECM and while the engine is running, tap on the ECM with the palm of your hand. Does the engine run any different or act like it cuts out while tapping? Next would be ECM grounds. On the engine and/or trans there will be several ground connections. Make sure EVERYONE you can find(look thoroughly!) is clean and tight. If in doubt, remove each one, sand the terminal and its contact surface. I can't stress enough the importance of the ECM grounds!! It doesn't take much resistance to cause the ECM to do some strange things.
Sorry for the lengthy instructions, but if you follow all of it, you should be able to find the problem. There are a few other things you can do too, but I'll let you do this stuff first.
Good luck and post what you find.
Spark...make sure you have plenty of it at the plug itself. Best bet is to use a spark tester, like a "ST125" or similar. Most auto parts store carry them. Be sure to check every wire while the engine is running. Shut the engine off each time you move the tester to another wire so you don't get zapped. The old screwdriver trick will work but it's not 100% foolproof, the ST125 is!! Look inside the dist cap for moisture, corrosion or carbon tracks. Just because it's fairly new, doesn't mean it's not the problem. Same with the rotor, is the tab in the center clean?
Fuel...put a gauge on it to verify pressure. I think it should be about 9-13 psi, but I'm not certain. Check the manual if you have one. Another thing you can check is the injector(s) in the throttle body when the engine is running...you might need a helper to assist in all the start ups so you can stay under the hood and check everything. Is there a good cone shaped spray pattern with no drips? If it has 2 injectors, make sure both are spraying the same.
Air intake and exhaust...remove the air filter, sometimes it's easily overlooked. Use a light to see if it's clean, but removing it will prove if it's the problem or not. If you haven't checked the exhaust back pressure yet, at least make sure you can feel a moderate amount of pressure coming out the tail pipe with the engine at about 2K rpm. Connect a vacuum gauge to a vacuum line or use a 'T' and see what you have for a reading at a constant rpm(I know it might be tough to get a steady rpm), and be sure the needle is steady and not fluttering...I believe this engine is known for eating camshafts?? A compression test might be useful too. If you can narrow the problem to a specific cyl it's worth checking after verifying spark and fuel, but hold off for now.
Running rich or lean...since you don't have a scan tool to read engine data, do this. First create a large vacuum leak, the brake booster or PCV hose will work. If it runs better, the vehicle is running rich(pressure regulator maybe?). Next disconnect the Map sensor if you know where it is. Pull the vacuum line from it or remove the sensor from the intake and plug the vacuum leak off. If it runs better, the vehicle is running lean. You could also unplug the coolant sensor for the ECM, but using the Map sensor is more accurate.
Last but not least...ECM or connection problems. If any sensor was at fault, most likely the check engine would be on with the engine running and a code would set. Locate the ECM and while the engine is running, tap on the ECM with the palm of your hand. Does the engine run any different or act like it cuts out while tapping? Next would be ECM grounds. On the engine and/or trans there will be several ground connections. Make sure EVERYONE you can find(look thoroughly!) is clean and tight. If in doubt, remove each one, sand the terminal and its contact surface. I can't stress enough the importance of the ECM grounds!! It doesn't take much resistance to cause the ECM to do some strange things.
Sorry for the lengthy instructions, but if you follow all of it, you should be able to find the problem. There are a few other things you can do too, but I'll let you do this stuff first.
Good luck and post what you find.