My first instict with slight missing is usually to go right to ignition and checking the wires and spark plugs. Pop up the wires and see if there is any oil in the holes and check the plugs for a messed up tip. That would have been the first thing for me.

However after more posting that you brought up, it seems that may not be the issue (something to check non-the-less). But going by the codes that happened to come up, im gonna say there is a vaccum issue here. Either a bad vaccum line, or one of the emmission control sensors is not working properly

 

ok i dont now about the other guy but i need help with the same subject. i have a 97 eclipse gs n/t , the timing belt had a rattle noise so i thought okay im going to do the head gasket, water pump and the whole shubang. well everything went okay did the work cranked up was fine let it clean all the stuff out for like 30 mins or so and then it would idle like its suppose to. but over time or the more i drive it at a red light it would start to drop in rpms and start to shake. it would even drop to about 200 rpms or just shut off. even at 800 rpms you can somewhat feel it shake alittle bit. any ideas?