It sounds like you might have a dirty or faulty MAF. Have you tried cleaning it? Take the MAF off (I assume you know how to do this if you know how to replace a coil pack!) and clean the sample tube out with QRC MAF Cleaner. Please do not use anything stronger than electronics cleaner; those wires are very sensitive! Don't use carb cleaner.
The problem is, it's so hard to troubleshoot a low RPM stumble as there are SO many things it could be.
The popping through the intake makes me think you're running rich, and/or that your timing bight be off.
Since the timing is electronically controlled, the only thing you can do is to check the timing belt to make sure it didn't skip a tooth or two. They will do that as they get old and worn out.
Have you run your engine codes to see if they say anything? Just because your CE light isn't on doesn't mean you're not getting codes. Also, your CE light might be burnt out!
check these things and let us know what you find out.
