any idea what the difference is between stock 5L injectors and the ones on an EB GT?

EB GT, ED Sprint and EL GT all ran 24lb injectors (blue tops) compared with the stock engines which got 19lb (orange tops).

what would the effect be of running a standard airflow meter/MAF/whatever with the 24lb injectors?

You wouldn't want to, it will just run too rich. And if you are still running the stock MAF, there is no need for larger injectors really.

just asking on behalf of a friend who's running a ford motorsport MAF/pod combo that's calibrated for stock injectors on his EB GT

On the EB GT it will be reasonable, still not a great idea though. The EB GT EEC is calibrated for 24lb injectors and the MAF curves between stock and GT aren't too far off so the EEC will probably compensate enough.

BTW the only Ford MAF that really works with stock injectors is the cobra 70mm MAF which is the same as the GT one anyway. If it is a calibrated unit then it is probably a Pro-M or GMS unit I would think. He could always get a Tweecer which has EB GT support and then he would be able to tune the injectors and MAF properly, not to mention the rest tunign it will give.