Since this started when you stopped the file transfer, is it possible that space was reserved on the MacBook Pro, essentially leaving you with not much available free space? Some backup programs behave that way. General rule is that you want 10% or more of your disk capacity free for systems usage. Much less than that and the system can slow to a crawl.
In your post, it says your MacBook Pro is using 10.6 Snow Leopard, however you're using a Mountain Lion cache cleaner? What operating system are you using?
That's simply what the program is called. It's meant to work on older OS's.
Yeah that was probably the problem. There was about 15GB out of 160GB left, and I was attempting to fill the rest.
Funnily enough, the MBP started working fine on a restart about 15 hours since the symptoms of slowness started showing. This is weird, but I took no chances and made a complete backup anyway.