HT202731 Unstable operation when 2 or more USB devices connected to usb port on a MacBook Pro running Yosemite

I have tried connecting a number of devices to my MacBook Pro but I have found if I try to connect 2 or more using either usb ports or a usb hub the computer reports 'disk not ejected properly' and sometimes it will fail to recognise the device and remove it from the desktop or it stalls operation and I have to turn the computer off at the power button.
I have tried erasing the hard drive and reinstalling the operating system.
I have done various types of reset suggested by apple support.
The computer has been to an Apple dealer who has tested the hardware but found nothing due to the intermittent nature of the problem.
I have operated the computer with only the software originally installed on it present.
Could it be possible that a virus could be present on the usb devices I am trying to connect?
My computer is a MacBook Pro (13-inch, Mid 2012)
Processor 2.5 GHz Intel Core i5
Memory 4 GB 1600 MHz DDR3
Startup Disk Macintosh HD
Graphics Intel HD Graphics 4000 1024 MB
Operating System X Yosemite 10.10.1
Devices I have connected to USB ports all USB 3.0 compatible in a variety of combinations:-
7 port superspeed USB 3.0 hub (powered).
4 port Inateck USB 3.0 portable hub (not powered).
Buffalo ultra portable 500Gb USB 3.0 hard drive.
Seagate Expansion portable 500Gb USB 3.0 hard drive.
Seagate Expansion desktop 2Tb USB 3.0 hard drive (powered).
Seagate Expansion desktop 3Tb USB 3.0 hard drive (powered).
ScanDisk Cruiser Edge 16Gb USB stick.
ScanDisk Cruiser Edge 32Gb USB stick.
Hewlett Packard 16Gb USB stick. (This causes an instant crash now.)

Why?
- Because when I'm editing/ rendering lots of HD video everyday, I don't want to share system resources between virtual machines... I want the entire system's resources devoted to what I'm doing.
- I don't want to spend anymore money than I have to in order to buy one of the faster virtual systems. Not to mention, I've had a bad experience with Parralels in the past and I'd rather not use one again.
- I really don't want to clutter up my system anymore than I have to for a project that's only going to take a few weeks.
- I don't mind swapping hard drives... it takes two minutes, and I have an empty ssd just sitting on the shelf.
So, back to my original question. Can I just swap the computer's drives, then install Ubuntu on the second drive and be good to go without any harm to my MacBook Pro or OSX on the other drive (which wouldn't be connected when Ubuntu is running)?
Thanks.

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HT202731 Unstable operation when 2 or more USB devices connected to usb port on a MacBook Pro running Yosemite

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