Hi Allen, shrinking is exactly what you need there, and you are right, bending the edge isn't going to help. The hard part is that shrinking on 2024-T3 is not easy, and some folks consider it not safely shrinkable. It will require some practice and possibly some modification to the tool. If you do decide to try, absolutely practice on lots of scrap material before you practice on real parts, and keep in mind it is a very subtle change you are trying to accomplish.
These aluminum sheets have been heat treated, which gives them their required strength, but that also makes them more susceptible to cracks and problems caused work hardening. Also, the teeth on the shrinker are very coarse and will leave marks in the soft aluminum, which you will need to remove. Doing so will also remove the alclad and necessitate two-side finish application before final assembly.
There was a time where more gentle aluminum-oriented teeth were available for purchase, I think from Kent White, but he has died and I'm not even positive it was him that was offering them. If you could find some, it might be worth the investment.
Another option is to stick 150-ish grit aluminum oxide sandpaper between the aluminum sheet and the shrinker teeth. This will buffer the sharp teeth against the aluminum and reduce the amount of post-shrinkage dressing that will be required, but the sandpaper will be consumed over time so keep an eye on it.
When it comes to using the machine, use light pressure with each pull, and move the material frequently to a new spot. You are wanting to make a whole bunch of tiny shrinks, vs a few big shrinks. This will allow you to get the desired shrinkage movement while minimizing localized work hardening. The part of the metal that actually gets shrunk, at least on my tool, is about a quarter inch- whatever the gap is between the teeth when they are fully open. Don't be distracted and think that the shrunk area is as wide as the whole teeth- like 2", indicated by the tooth-mark damage to the sheet. To fully diversify the shrinking zone, you only need to move to a new spot as wide as the jaws open tooth gap (1/4", not 2"). Let me know if that doesn't make sense and I'll try and draw a picture.
Also, mark on the boot cowl where your actual bubbles are, and only shrink those zones. Don't shrink the full edge of the sheet. If you are doing it well, you should probably be installing and removing the sheet a few times as you go, testing the fit. This is definitely a sneak-up-on-it situation because of the negative impacts of the shrinking (damage+work hardening), and if you over-do it, the piece will still not fit well, in a different way.