Shutdown is a problem that still has no solution, i had been trying to solve since the beginning, but no joy.
"sleep and the internal Speakers" <---- These have to be working if you are using my DSDT and the ToshibaHDA.kext for audio, remember to erase AppleHDA.kext and the caches (System/library/caches/com.apple.boot.caches/startup)
For the usb ports still giving power on sleep, remember that our laptop has the function "sleep&charge", you can change it on bios, i have it always on cause i recharge my devices with them.
Bluetooth always fails after sleep unless you patch bluetooth transport, adding a 5 second delay to bluetooth startup (Can´t find the link for the thread, sorry).
Try this things and post results.
Also, Yosemite is buggy as hell, i hope 10.10.3 solve some errors with hanged services.