How does it do without the filter on it at all? I’m wondering if having the MAF so close to the cone it isn’t picking up a leak or a spot in the cone where air is coming through faster.
Think of it like a like having pulling the release pin on an air compressor where all the air comes out one hole at extreme velocity and that is hitting the MAF and skewing the results.
If you have access to a OBDII cable and Scantool.NET you could check the readings for MAF and maybe fuel trim. When the car heats up the O2 sensor takes over a large portion of monitoring the air/fuel balance. If this car does not have a heated O2 sensor it may take longer for this to smooth out.
Another idea is see if you could put something to slightly diffuse the air coming towards the sensor element. Or if you could somehow re-engineer this so the MAF is closer to the intake manifold but not in the way of the oncoming vent gases coming from the valve cover since that could deposit on the MAF element and damage it.