I have one real problem remaining with my mac. I am running 10.11.3 but this problem has stuck with me from earlier builds. I am using a recent USB injector from Rehabman, and have disabled a few ports to get under the 15 device limit. All the ports I want working are working still no "red" 3.1 or type-c 3.1 ports, but thats ok since I don't have any of those devices.
My problem is that if my computer goes to sleep with a USB drive plugged in, I get the improperly ejected message. I think there could be a DSDT edit for this problem to mark the USB ports as internal or something, but I don't have a good idea about that. Does anyone know what edit I might make so that USB disks don't get ejected on sleep (or if they do get ejected it is properly) I see there are some scripts that can be set to run to eject disks before sleep - but I would rather figure out how to configure the USB ports properly so they act normal.