Id injector data question

I've noticed when I input injector data in, Say on a boosted car, with larger 5" intake, I have to decrease the Maf transfer function to reach my targets in Pe table. So on an 6l80 auto vehicle, this could pose problems with shift pressures. I would just redo the Virtual Tq tables, and add shift pressure and adjust shift timing in the trans section. I was told you should alter the ifr rate in the tune so that I would should increase the Maf transfer function only, not reduce it anywhere due to reducing the estimated load. Also was told you could adjust the fueling with the Pe table, and the stoich tables. My question is when I input Id's data, shouldn't it be correct data? I'd assume the 5" intake makes the need to decrease the Maf in certain parts to hit my Pe target? Thus leading to adjust Virtual tq higher than normal. What are your guys experiences with this? I'm not a fan of tuning the fuel with Pe table, or stoich tables. But having to alter my Id Ifr data seems backwards. How are you guys getting correct load when using a larger than stock intake tube diameter?

Yeah, I understand that with a larger intake the air volume is higher with lower velocity through the Maf. Hence why I'm having to decrease the Maf transfer function to hit my commanded. Honestly, I'd rather leave the injector Ifr with what comes from ID, and tune the Virt Tq. tables and trans pressure to get closer to what it actually is, but maybe scaling injectors with a larger intake is a better way? Some people have recommended leaving the Maf curve stock and getting commanded lambda with the Pe tables, Stoich tables, and Eq ratio. So Eq ratio and Stoich table changes seem, they'd be pretty similar effect? And Pe table trim for rpm base fine tuning? But with a stock Maf curve, I'm still going to need to modify the Virt. Tq tables to get increased trans pressures, or just tune the trans in the trans section. I generally just do the trans pressure and shift timing seperate.

Tried to edit my post on mobile and it got deleted.

Anyhow, let's take a step back. You will have to INCREASE your maf transfer function for the reason that more air will be flowing over at a given hz. What injectors and ecu are you working with? If you do anything but half ifr, double stoic, half ivt you're causing more work for yourself than is necessary