Yeah, that happens. I wonder if you could run a bypass pipe around the MAF, halving the amount of air that goes through the MAF and then adjust the fuel (say, the injector constant) to put in twice as much fuel as it "thinks" it should have? Sounds dubious but could work.
Alternatively, you could build a MAF out of the guts of a 2" into a 3.5" body. You'd need to retune but it would likely work to some degree.