UPD: There is no need to "clean" the OS in general unless there is a specific problem.
UPD2: No.
As for the flash, I do not know. Any external needs a bootable install of your OS on it. You boot from it and then work on your internal from the external.
I assumed you also wanted to sell it since, at some point, you said something like you had the same problem as the other poster.
As for the external bootable clone: I have several external hard drives and at least 2 copies of every OS scattered over them. They are all bootable and the best way to resume working if something goes wrong.
As for that "windows" window, I have never seen anything like it, so this is not my area of expertise and have no clue how/where that is coming from. If you can't work on your internal and the external won't, my suggestion is to contact Apple tech support and/or take it to your nearest Genius Bar for a diagnosis and help.