I have a very similar situation. We live in a 1/2 acre with neighbors on all sides (well, the two adjacent homes are now repos, but still have people in front, rear and diagonal in all directions. Our roos sleep in the hen house all night (window open during summer), but come outside around 5:30- 6 am.
Anyway, most of my neighbors keep their windows closed with air on as well and many said they didn't even notice we had roosters (we have several!). Maybe it is because the dogs in the neighborhood are loud...who knows.
Chances are, the only neighbor that is really hearing them is the one that is leaving her windows open and it may because she is having trouble sleeping anyway (if I wake up for other reasons and listen, I can hear my roos too). The winters will be easy since you will close the windows, but the warmer months...well, here are a couple options that may help. Was your neighbor complaining that the roo wakes her up or was she just being polite and letting you know that he is crowing in the wee hours?
1) add sound proofing to the walls and roof (inside). This will help reduce noise.
2) on the outside of the coop, add wood window covers that attach at the top of the window. Have it propped open to 45 degrees (or a little more...still better than open completely). This way it blocks direct sun or light (such as car headlights, which can set of a rooster) and it also helps direct sound towards the neighbors. Since you have glass already, the window cover can be a permanent fixture or you can make it hinge and it adds as wood covers for hurricane season.
ETA: I agree about taking out the odor part in the letter (unless it is too late, of course)
). Some neighbors will see one fly and immediately blame the chickens, so I think it's best to not plant the seed.
If they're never gonna smell anything, don't bother bring it up. Their dogs poo can stink too if not cleaned up.