Glad to hear you found it. Just a thought but as the bike ages, these nuts will continue to be a problem now and then- might be worth grabbing a package (5 I think) just to have on the shelf. It is easier to buy them in advance and have a few on hand than it is to order and wait for them while the fairing flaps in the wind.
In a pinch, you can also borrow either or both a fastener and / or a well nut from another location; I have taken the fasteners from things like the small cover just behind the saddle and used them on the front fairing in a pinch. The rear part is not critical and will not be loose even missing one fastener while the front fairings are more sensitive to one missing fastener.
Brian
Took my left side apart again and looked closely with a flash light. Finally found the bugger wedged sort of underneath the coolant tank. Plopped it back on the fairing and good to go. Thank you all!