Just a shot in the dark...does the car have stock 19lb fuel injectors? If you have aftermarket injectors the speed density cars wont run right.

And like GNS said i would check the fuel pressure...

Also you said you did cap and rotor and plugs etc... Did you replace the ignition coil? That could be the issue... When was the last time you replace the fuel filter? a dirty/clogged filter could do it too. It may also be dirty/clogged fuel injectors?