Going back to the issue that I started this thread for, when I rebooted to test the boot optomization just mentioned, I had a lot of trouble booting back to desktop, just as before dealing with the USB 3 issue. This leads me to believe that my booting issue is not due to the USB3, because disabling the USB controllers in the Device Manager did not solve the problem.
On the next boot, I entered my password for login, but when pressing the enter, nothing happened. I tried it again with the same effect, so I booted into safe mode without any problem. I disabled all of the items on the startup tab in msconfig, and tried again. That time it accepted my password, but never got past a black screen. Another reboot and I finally got to desktop, but it took several minutes for my browser to open.
Obviously the issue remains, and all that I can think of is to disable a couple of services in msconfig, like the acronis scheduler, and firewall. Before doing any more experimenting, I wanted to post this, so that if anyone has any ideas on the subject, that I would be able to read them, since I don't know how easy it would be to reach desktop again.
Oh! One thing more, back on that first boot attempt, the BIOS couldn't detect my C: or H: drives. After doing some fiddling with the data cables, and leaving H: disconnected, C: returned to detected in the BIOS.