You can't just throw the MAF into something it wasn't built for. This is what is happening.
The MAF only measures the airflow at one point inside the pipe, not the entire pipe. The MAF sensor takes its measurement as a voltage which is then sent to the computer. The computer then uses an internal conversion made specifically for that pipe diameter to turn the voltage into something useful, grams/second.
So what is happening is because you increased the diameter of the pipe, the ECU thinks there is much less air flow than there really is. This will make it cut fuel so as to prevent unburnt fuel (smoke). In reality, the engine is just burning super lean.
Here's what you can do.
1. Use the stock MAF housing (easy).
2. Tune the MAF to the new diameter (not easy).
3. Chip the MAF sensor (not easy, and don't do this).
4. Run without a MAF (needs tuning, not easy).