Weird USB / sleep issue; what can I do?

This is an ongoing issue that has been popping up since at least as far back as 2012, possibly further. It never made sense, and I've slowly pieced together some strange occurrences that might shed some light on the problem.
Back in the Fall of 2012, I copied some data onto a USB thumb-drive from my laptop, then a 15-inch MacBook Pro (I bought it used, I think it was 2006 or 2007 vintage). There was a large amount of data transferred. The copying process took about half and hour. I took the thumb drive to a friend with a much newer computer. My friend told me the transfer took a few minutes. I knew something was wrong then. The MacBook Pro was running MacOS 10.6.8.
The MacBook Pro died March, 2013. I was able to hire a specialist to extract the internal hard disk from the laptop, put it in a USB case, and transfer the contents verbatim to a newer machine; I had to buy a refurbished late-2012 iMac. running MacOS 10.8. (Now runs 10.9)
I have noticed peculiar behavior in running this iMac. USB thumb drives and other USB hard drive transfers can occasionally seem sluggish. Weirder still, if I put the iMac to sleep overnight, waking it up in the morning causes a very strange "wake up" process where the display is greyed out and a progress bar lets me know it is slowly waking up. This wake-up process takes one to two minutes. This only happens when there are no USB peripherals connected to the iMac. If I put the iMac to sleep with a thumb drive plugged in, it wakes up instantly.
I have long suspected the iMac had some kind of software bug or corruption that was brought over from the MacBook Pro in March of '13, when I hastily transferred everything over in the midst of the laptop's breakdown crisis.
Recently, I ran Software Update on the iMac to get Epson and Security updates installed. I repeatedly was greeted by the warning message: "System extension cannot be used The system extension "/System/Library/Extensions/AppleUSBEthernetHost.kext" was installed improperly and cannot be used. Please try reinstalling it, or contact the product's vendor for an update." I have no idea what this means, but it does seem to confirm that there's some weird bug loose and it has to do with USB.
The only question is: what can I do about it? Would calling AppleCare for advice help?
I am my own "Chief Cook and Bottle Washer", in that I do my own I.T. most of the time. I've been using Macintoshes since 1986.

Hi Walt_Atwood,
I'm sorry to hear you have been dealing with this issue for so long. If you are getting error or alert messages about a deep system file (like a System .kext), you may want to try reinstalling your OS. This should not affect your files or user settings (as noted in the following article), but just to be safe it is alway a good idea to have a backup of your data prior to these kinds of troubleshooting steps.
OS X Mavericks: Reinstall OS X
OS X Mavericks: Back up your Mac
OS X Mavericks: Alternatives for backing up your Mac
Also, regarding the unusual wake up process that you noted, from your description it sounds like your machine is waking from Safe Sleep. This may be normal for your model (Late 2012 iMac) if it has been asleep for more than 4 hours and there has been no USB activity:
Mac computers: Progress bar appears after waking from sleep - Apple Support
Regards,
- Brenden

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