I fail to see how you've damaged anything assuming you're not seeing brake fluid leaking. Changing pads and rotors is crazy easy and really difficult to screw up. If you screw it up, usually things don't back together correctly and/or you get lots of noise and the wheel likely won't move freely.

Toyota brake pedals have total crap initial feel. I've noticed this in all Toyota rentals I've had and my wife's 2020 4runner is the same. It always takes me a few minutes to adjust to the 4runner's pedal when coming from my BMW M235 or Outback 3.6R. When you initially depress the brake pedal on the 4runner, there is a hiss/suction/swoosh noise as the pedal travels 1/2" before I feel any real meaningful bite from the brakes. This goes for every Camry, Avalon, RAV4, Venza, etc. I've rented in the last decade (and there have been many).

I think the sound you're hearing is normal; you've just now paid attention to it because you had never changed pads/rotors and and you're worried you did something wrong.

There is absolutely no reason to flush the brake fluid on a rotor and pad change. There's also NO possibility of air getting into the lines during a pad/rotor replacement assuming you didn't open the bleeders or let brake reservoir was super low or slice/break a line.

As for weak brakes, the likely issue is the rotors and pads need some bedding. When you replace pads and rotors, brake feel on the first drive can be scary. Brakes really come to life after you do a few hard braking events. I'd do 3 to 5 50mph to 10 mph back to back near stops and then drive to cool off the brakes. You'll be surprised by the increase in bite and feel once they are bedded.

Did you clean the rotors with brake cleaners or some other solvent before installing? The rotors have a rust inhibitor that should be removed before install. If you don't remove it, it can make braking real sketchy and weak. The inhibitor can get into pad and will take a long while to burn off. Again, you'll need to do some hard braking to get them really hot burn the stuff off.