As for your first question about the stock Intel cooler, as long as ur not over clocked which I see you say you are not, then it'll do, I've got a 4770 with stock cooler, according to fan expert 1100 rpms is the slowest the fan can do, and can go as high as something like 2000-2400rpms, so as long as your temps are good, then the coolers working fine, if you wanna go different cooler there are cheap yet good after market ones like cooler master hyper 212, or the noctua one, can't remember the numbers on it, but they'll cool better then the stock one allowing you or the system itself to spin the fans slower more of the time
Your second question, 1 minute boot times, sounds close to being right to me, for really quick boot times you would need an ssd as your boot/os drive, also the type of mechanical you have would matter as well, sata 3 faster then sata 2, sata 2 faster then sata 1 or plain sata , the Intel delayed start your talking about I'm assuming is somewhere within the Intel rapid storage technology in which case a lot of that program is specifically for speeding ssd's up
Third in not really sure about cause on my board at least, plugging in my mouse when it registered as a user input it doesn't turn itself off, I'd say you may wanna try leaving the option you said temporarily fixes it, and uninstall the mouse, restart windows with it still plugged in and windows will try to load drivers itself on next boot as long as ur connected to the internet, after that you may wanna head to the mouses manufacturers page and see if they have any drivers or software for it although if its USB you shouldn't need them really
As for your drive question I'm not really sure what your asking lol what drives were a b to install, and what and why do you need a driver update for it, Asus does have an app called ez-update but as I downloaded all newest drivers right from Asus support I've never had to use it so I'm unsure of what it actually updates
CoolerMaster HAF 932 Advanced/ Maximus VI Formula/ I7-4770K/Swiftech H320/ Corsair HX850/ G.Skill Trident X (2x8) 16gb 2400MHz/ 2x 840 EVO 120gb(Raid 0)/ WD 1TB HDD (Backup/Storage)/ EVGA GTX 1gb 560 TI/ Asus 12x bluray combo