I'm not familiar with these diesel platforms yet but lots of gas engine experience and maf sensors are very finicky. Being that I have swapped intakes yet I'm not sure what sensor goes where so this is coming from troubleshooting the gas engine side of things. Just making sure but does your new intake setup require any type of tune to work properly?
1. Check and make sure maf sensor is pointed in the correct direction, they typically have a flow arrow indicating which way to install them and the mounts usually allow them to be installed one way only
2. Being that there are two sensors make sure they didn't get switched around and that they are in the proper locations
3. Make sure the plugs/ connectors are fully seated and that they are locked (if equipped)
4. Check all clamps, filters, boots & connections make sure they are properly tightened and not overtightened as that can distort things and allow extra air into the system
5. Do a visual check and make sure the sensors aren't damaged or picked up debris along the way and that the gasket is in place. A missing gasket will allow in additional unmetered air
6. I've seen others mention that there is some sort of foam in the air box or air tube somewhere (sorry, back to the I haven't taken one of these apart yet excuse, lol), make sure it hasn't become dislodged and plugged the tube or turbo inlet
When a maf code is set it can be from a sensor in backwards, unmetered air getting into the engine, connector/ connection issue, loose clamp and or filter, blockage, damaged sensor, sensor in backward.
If all of that looks good put it back to stock, reset it and see what it does. What type of air filter is on it? Is it an oiled filter? If it has too much oil it could have gotten on the maf and that will cause an issue. Too much oil could also potentially restrict air flow. They sell specific maf cleaners, you can always try cleaning them but don't overdo it, try not to completely soak the whole sensor.
That's my free advice, if I think of anything else I'll reply. Good luck and post what you find!