I've tuned cars with all the honeycombs out of the MAF, and the airflow signal is unsteady, and the recovery is sometimes bad, but other than that, it's normally not that big of an issue. Of course, these cars also have fuel control, and I've dynotuned them all, but a few of them were setups very similair to yours. Again, I think when you take the big honeycomb out, it's pretty much hit or miss, cause I've seen it go both ways. Have you checked the plugs yet?