Hello! There are several reasons why this code may set.
First, if the filter is dirty, it usually doesn't make it run lean, unless the filter has allowed dirt to reach the Mass Air Flow (MAF, often called an Air Mass Meter) sensor, or if the air filter is really oily, it may have also contaminated the MAF sensor. If this is the case, you can sometimes get lucky and carefully clean the end of the MAF sensor with brake cleaner.
Also, since you do have a cold air intake, make sure all of the duct work to the throttle body is intact and all the clamps are tightened. Also make sure any hoses that were hooked up to the original air intake, still have a place to go (you can't have any unconnected hoses or nipples).
Vacuum leaks are common with this engine, and the BEST way to check for them, is to install a smoke machine. I know most consumers won't have one, or even have access to one, but its truely the best way.
Another common issue is the Crankcase vent system. To tell if its failed, you can usually remove the oil fil cap and feel an excessive sucking from the oil fil (sometimes the engine will die if the vent system is bad when the cap is removed)
The filter would have to be pretty clogged up, to cause those codes. If its been a real long time since the filter was replaced (or you don't know its ever beend one), then you may want to replace it as some preventative maintenance.
Check the hoses very carefully, especially the ones between the MAF and the engine. Sometimes leaks are hard to see, which is why the smoke machine is an invaluble tool! On these cars, I haven't had much luck spraying carb cleaner around the intake and hoses to diagnose, that trick works well on other engines. You need a fast scanner to monitor quick changes in fuel trims for that to work.
Crankcase vents are common, but the fact that removing the cap made little change doesn't support that theory. Usually when they are bad (in my experience) removing the oil cap makes a big difference. There shoudl be some vacuum in the crankcase, but how it should feel is something I can't describe.
If there are no vacuum leaks, then you probably have a bad MAF ( not all MAF sensors benefit from cleaning).