I have some MAF cleaner, I'll give it a good cleaning.

I would have thought the tube style MAF would be accurate regardless of intake configuration, but I read otherwise. Like I said, I'm new to MAF stuff. If you're certain that doesn't matter...I'll believe you.

Mods consist of an intake tube and a muffler, so I would agree the VE should be pretty close. The fuel trims change quite a bit now, but maybe that's all influence from MAF.