Interesting.... that is a fair amount of miles. Nothing crazy, but add that many miles to the extra stress of an APR K04. Have you ever changed your timing belt? Others may be able to chime in, but could a missing tooth or even a "stretched" timing belt lead to some of these issues (ie, more pronounced at higher revs)? Again, I'm really surprised your vehicle isn't throwing a CEL. Another idea is to make a YouTube video of the problem and then link it here. Actually hearing what the car is doing may be very helpful. That's just spit balling a bit, but it would be very helpful to at least know how it acted using an OE intake as a control experiment... especially since it's so hard to know the specific tuning on a modded engine like that and how much it's telling the MAF to read regarding air pressure/density. Obviously, the MAF being bad is still a possibility as well (or even a combination of issues with the non-stock intake)... but, again, I'd expect it to throw a CEL if there was a MAF issue.