I'm not specifically familiar with how it's done on Hondas, but all auto windows have adjustments inside the door which you can access if you remove the inside door panel; you can "jack" the window in various directions for the purpose of making it a snug fit in the window track. That would be the first thing I'd try ...it would be nice to have a factory shop manual or at least a specific instruction for you to follow which tells you where the adjustment is and which way to turn it. I know where to get that for my Toyota, but have no idea on the Hondas.
On the brakes ...what pads are you using? Are they original OEM pads or aftermarket pads? Some pads are known to squeel a lot more than other pads, especially if they are harder intended for "long life", that's the tradeoff. Also, most pads have "anti-squeel" shims required between the pad and the mounting in the caliper. The shims have to be installed exactly correctly or you get squeel. If the rotors are in good shape, those are some likely causes of squeeling.
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