Alright, let's start from the top. To do an engine once-over, you'll need to get your hands a little dirty, and be on the lookout for anything that looks unusual or out of place. Start by checking all of the vacuum hoses. You have several to check. Get in close with a trouble light and look for cracks and rotting. Run your hand along the entire length of hose, feeling for anything unusual. The hose should feel smooth and rubbery, like a tire, but much more flexible. If it feels dry, rough, spongy, or cracked, it needs to be replaced. Do this with all of the vacuum hoses.
Check a few spark plugs. You don't need to do them all, since 4 are fed by one injector, and the other 4 are fed by the other injector. The plugs on the driver's side are easy to get to. Check them for any signs of problems in the engine. Take 2 or 3 sparkplugs inside to your computer. Go to this website
http://www.fitchfuelcatalyst.com/techinfo/tuning.html
and scroll down. This will teach you how to read your sparkplugs with good pictures. Check the routing of all the plug wires to their respective plugs. Remove the plug wire from the plug, and look inside with the trouble light. If the inside of the plug wire is corroded or broken, it needs to be replaced. Make sure the boot is firmly seated on the plug. This is the firing order. Make sure all the plug wires go to the right plug.
Start with this, let us know what you find. Check the codes as well and we can tell you what they mean. You might just need a good tune-up, in which case, we can help you with that as well. Good luck!