I use Pythonista on iPad mini (iOS 6.1.2) and I have never had any of the problems you describe. Just went and "double checked" your list. Have you tried to "kill" the program entirely (even cold boot of the iPad)?
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Latest posts made by PyLot213
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RE: Malfunctioning iPad Keyboard Scrollingposted in Pythonista
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RE: Separate Filesposted in Pythonista
Also FYI: If you want to structure your stuff even more, then you can also have your file in a different folders (since the import follows the python import rules). The only thing you have to do is create an (even empty) init file in the directory and then you can import it like
import mydir.mycode
(you can read more about it here: http://docs.python.org/2/tutorial/modules.html#packages )