I noticed that USB mouse/keyword worked in the recovery mode every time. The problem is that I end up with crappy graphics mode in recovery so I basically just force the normal boot to go through recovery by adding "recovery" to the GRUB_CMDLINE_LINUX in /etc/default/grub. My line looks like the following:
GRUB_CMDLINE_LINUX="recovery acpi=force irqpoll usbcore.autosuspend=-1"
along with all the options that I have tried and failed. I also tried the following (from another askubuntu question), which worked for some time:
sudo powernap-action --disable usb_autosuspend
However, I think "recovery" is the only thing you need. You had to press enter a couple of times to continue booting if you go this route, but at least USB works on boot and you have good screen resolution.
PS. I had this problem with Ubuntu 14.04, and after switching to Mint 17, had the same issue. I tried various options, some worked for a while and then stopped working, but I eventually ended up with this really frustrating problem reboot after reboot. I don't believe this is a hardware issue, or I don't believe this is a hardware issue that Ubuntu cannot work around. My dual-boot Win7 had no such problems whatsoever. I was pulling my hair out and seriously thought about abandoning Ubuntu based distros.