If you're going to re-glue the window, i'd use crazy glue gel (dont use regular crazy glue, it will burn through the plastic window).
Take a picture of the storage lid, i'm not sure how you mean.
In regards to cigarette smoke. Most cigarette smoke smell is kept in the headliner. Since the car is a vert, and i'm assuming you find that is smells with the soft top on (which wont absorb too much smoke), so you likely have a bunch of ash in the bottom carpeting.
If i were you, i would:
-Wet carpet vac all the carpets in the car
-Run a dehumidifier in the car overnight
-Then steam clean the carpets
-Buy a product called ZEP smokescreen. (you can buy it directly from zep, who are in toronto[edit: nevermind, you're in atl], but for a wholesale purchase you gotta spend 35$ afaik) and dump that stuff in the interior (its an aerosol spray.) Make sure you do not inhale it, and once the car's interior is full of it, seal the car up and let it sit for a few hours.
-Run dehumidfier again.
I like running the recirculated air while the zep is in the car, cleans out the airways in the hvac nicely.
Its a bit of work but if the smell of cigarettes bothers you, its worth it. Home hardware can rent you a carpet vac and a steam cleaner
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