Normally, those Pan head allen key shoulder bolts are used for the fairing - the shoulder is to stop you clamping the fairing plastic. They normally tighten into a captive thread. That is quite a large shoulder so will go through a thicker part of the fairing - like this one for the underbelly.
90113mm5000
Over time, those clip-on captive threads like 90312mt3000 get lost or cannot be used due to cracked fairing so another solution has to be found.
Google images for the number.
The shoulder bolt with the hex head has me stumped though. Again - something that needs to be held rather than clamped.
Last minute lightbulb - There is one something like that 90141sa7003 that holds the battery cradle.
None of these uses require nuts though. I think that you have 4 unknown pieces there, unless, as I suggested, a nut has had to be used instead of a captive thread.