A MAF's calibration is nothing more than how it has been configured to report air flow. The MAF transfer curve describes the flow characteristic of that MAF. Changing the MAF calibration is either done by altering the electronics that install on a MAF housing or by changing some mechanical aspect of the MAF housing, as is done with C&L calibration tubes.
From the factory, a MAF isn't calibrated to a specific injector. The MAF is sized to its application based on the max airflow the engine can aspirate. From there, the MAF flow curve, along with other parameters such as the injector slope/bp/offset parameters are entered into the stock tune.
In the aftermarket, you can purchase MAFs "calibrated" to specific injectors. These are sold as direct replacements into an OEM application when upgrading to larger injectors. In short, MAFs calibrated in this way reduce the reported airflow to the EEC by the same amount as the newly added injector flow will be with the upgraded injectors installed. As a result, the EEC will produce a shorter pulse to the injectors for the same engine load condition. While this seems like an ingenious way to avoid a professional retuning of the EEC, it is mis-informing (i.e. lying) to the EEC allowing the EEC to believe things about the engine that are no longer true. As a result, there are unintended side-effects. Those side-effects get more severe the larger the injector upgrade gets. For instance, an upgrade to 24lb injectors from 19s will likely be mild with mild to no noticeable side-effects. However upgrading to 42lb injectors from 19s could easily result in issues related to cranking, idle, driveability, and excessive spark advance due to the EEC being misinformed about the true load of the engine. For EECs that also control the transmission, you may also find you are burning the transmission up by relying on the "calibration" of the MAF instead of getting the EEC properly retuned for the upgrade(s) so the EEC controls the transmission shift pressure correctly.
The correct thing to do in these cases is update the EEC's tune about both the MAF and injector upgrade so the EEC is aware of just how much air is getting into the engine AND how much fuel the injectors can flow. With that, the EEC can not only control the fuel but also the other aspects of engine management (i.e. spark advance, trans control, cam/valve control, etc) accurately.
Now for the details...this is where things get a little complicated. What the MAF is responsible for is to tell the EEC how much air is getting into the engine. The EEC compares the amount of air being aspirated with the theoretical max based on the engine's displacement. This comparison can be thought of as the instantaneous volumetric efficiency or as it is called in the tuning world, engine Load which is datalogged as a percent. 100% Load means the EEC calculates that the engine is aspirating 100% of the theoretical max amount of air. Most naturally aspirated engines are not going to be able to attain 100% Load. Stock engines will generally be in the 70s at WOT. A modified engine with an improved airflow because of upgraded heads/cam/intake/exhaust can get into the 80s and in some cases even get into the 90s. I've heard of people that have datalogged Loads right up near 100% for very narrow RPMs right where the intake/exhaust tuning is optimal. In contrast, most any boosted engine will exceed the theoretical max airflow. Lightly boosted engines can get into the 120s. Heavily boosted engines with intercoolers and other power adders can get into the high 180s and some higher than that. Unfortunately with older EECs, Load is limited to 200%.
Now that you get the idea of what Load is, the problem of your MAF is lying to the EEC about how much air is getting into the engine should be a little clearer. There are LOTS of things in the tune that are based on Load such as target/commanded Open Loop AFRs and spark advance. If you have an EEC that controls an electronic transmission, then the EEC doesn't communicate just how loaded the engine is and will not have the transmission shifting as stiff as it should. Add to that if you are upgrading your MAF and injectors to support other engine mods (e.g. better heads, better cam, etc) then the engine is more capable than it was in stock form and thus even more capable of tearing a transmission up as well as itself if onto controlled properly.
So to overcome the negative side-effects of calibrated MAFs, don't let the MAF lie to the EEC. Modify the tune to know what the actual MAF curve is and what the actual injector flow capacity is. With that, the EEC can calculate Load accurately and everything related to Load gets handled correctly as well. So with a tuning device, it is no longer required that your MAF be calibrated to your injectors. You are free to run whatever MAF that can handle your engine's airflow capacity with whatever injectors can handle the fuel load, even if they aren't calibrated for each other. People using the famed 90mm LMAF do this. The 90mm Cobra or Lightning MAF (aka LMAF) is not "calibrated" for any particular injector when used on an older EEC. So anybody that runs this MAF is almost guaranteed to need a tune to get it to work correctly across the entire RPM/Load range. However when looking at aftermarket MAFs, the calibration is still a nice feature. Assuming you've sized your injectors properly, buying a MAF calibrated to your injectors ensures that your MAF will also be adequately sized.
That's the majority of what you need to be aware of as it relates to MAF calibration. But don't assume that all you need to do is update your tune's MAF curve and Injector parameters. There'll likely still be some MAF transfer tweaks just to get things to run right. Also with a larger MAF and higher Load capability, you may find you need to rescale a lot of the tables based on Load to handle increased Load values your engine may now be capable of attaining. This is particularly important when tuning boosted applications that push Load well above 100%. After all, the spark commanded at 75% Load is NOT what should be commanded at 150% Load (heavy boost). Many of the tune's tables will needs to be modified to handle this. To learn more about rescaling tables for higher Load values, check out this thread:What are Scaling Functions?
89 Ranger Supercab, 331 w/GT40p heads, ported Explorer lower, Crane Powermax 2020 cam, 1.6RRs, FMS Explorer (GT40p) headers, Slot Style MAF, aftermarket T5 'Z-Spec', 8.8" rear w/3.27s, Powertrax Locker, Innovate LC-1, GUFB, Moates QuarterHorse tuned using BE&EA