Just scale them both to work together. There are an infinite number of combinations of latency and MAF scaling that will hit your fueling target, but you'll notice that when you have the wrong latency, even with the correct final AFR (using MAF scaling to "fix" it), it will still run like crap (hesitating, afterlighting, etc).
Start with your latency close to what you think it should be, adjust your MAF to bring the AFR in line, see how it drives. Then adjust your latency by say 10% either higher or lower, adjust your MAF to bring your AFRs to target again, and see how it drives. If it's better than before, make another 10% change in the same direction, if it's worse than before then go back to your starting values and make a 10% change in the other direction. After a few iterations you'll kind of "home in" on the latency and MAF combination that drives the best, and you can start reducing your step size until you don't really notice any more improvement. It's a bit of work, but should only take a few days if you do it a couple of hours a day.